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/7916127/working' mkdir: created directory `/scratch/stefan/7916127/working/protonate' Storing results in /scratch/stefan/7916127/finished Working in /scratch/stefan/7916127/working /scratch/stefan/7916127/working /scratch/stefan/7916127 /scratch/stefan/7916127/working/protonate /scratch/stefan/7916127/working /scratch/stefan/7916127 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory 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 mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 1061 protomers created Coalesing and merging protomers 1031 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1050 protomers after new stereo-center expansion /scratch/stefan/7916127/working /scratch/stefan/7916127 Bulk generating 3D conformations all protomers in /scratch/stefan/7916127/working/3D mkdir: created directory `/scratch/stefan/7916127/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7916127/working/protonate/xaaaaah-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' 1051 3D conformations generated for 1000 compounds Building REAL250005044893 mkdir: created directory `/scratch/stefan/7916127/working/building' mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044893' /scratch/stefan/7916127/working/building/REAL250005044893 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044893 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044893/0 /scratch/stefan/7916127/working/building/REAL250005044893 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1 `/scratch/stefan/7916127/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC2CC2C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044893.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044893 none O=C(CC1CC2CC2C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 170, 201, 201, 201, 201, 201, 27, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 27, 27, 17, 17, 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: 758 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044893 none O=C(CC1CC2CC2C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 7, 1, 1, 1, 1, 1, 1, 1, 38, 38, 115, 135, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 115, 115, 135, 135, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044893 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044893 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `/scratch/stefan/7916127/finished' Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044893/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044893 Building REAL250005044894 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044894' /scratch/stefan/7916127/working/building/REAL250005044894 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044894 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044894/0 /scratch/stefan/7916127/working/building/REAL250005044894 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/2 `/scratch/stefan/7916127/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NOC(CF)=C1)C1=CC(=O)[N-]O1) `REAL250005044894.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044894 none O=C(NCCNC(=O)C1=NOC(CF)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 27, 38, 110, 110, 110, 189, 189, 189, 189, 201, 189, 1, 1, 1, 1, 1, 1, 8, 27, 27, 38, 38, 110, 201, 201, 189, 1] 201 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044894 none O=C(NCCNC(=O)C1=NOC(CF)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'F', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 12, 1, 5, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 71, 51, 13, 13, 1, 13, 1, 1, 1, 1, 1, 8, 1, 176, 189, 189, 189, 189, 189, 176, 71, 71, 51, 51, 13, 8, 8, 1, 189] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 14, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044894 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044894 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044894/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044894 Building REAL250005044895 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044895' /scratch/stefan/7916127/working/building/REAL250005044895 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044895 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044895/0 /scratch/stefan/7916127/working/building/REAL250005044895 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/3 `/scratch/stefan/7916127/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC(F)=N1)C1=CC(=O)[N-]O1) `REAL250005044895.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044895 none O=C(NCCNC(=O)C1=CC=CC(F)=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 20, 25, 67, 67, 67, 89, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 8, 20, 20, 25, 25, 67, 89, 89, 89, 1] 89 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005044895 none O=C(NCCNC(=O)C1=CC=CC(F)=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [87, 87, 53, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 87, 89, 89, 89, 89, 89, 87, 53, 53, 45, 45, 11, 1, 1, 1, 89] 89 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044895 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044895 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044895/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044895 Building REAL250005044896 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044896' /scratch/stefan/7916127/working/building/REAL250005044896 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044896 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044896/0 /scratch/stefan/7916127/working/building/REAL250005044896 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/4 `/scratch/stefan/7916127/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044896.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044896 none COC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 109, 194, 194, 109, 109, 45, 28, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 194, 195, 195, 195, 194, 109, 45, 45, 28, 28, 7, 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: 814 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044896 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044896 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044896/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044896 Building REAL250005044897 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044897' /scratch/stefan/7916127/working/building/REAL250005044897 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044897 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044897/0 /scratch/stefan/7916127/working/building/REAL250005044897 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/5 `/scratch/stefan/7916127/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005044897.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044897 none CCCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 28, 22, 16, 16, 16, 12, 9, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 22, 24, 24, 24, 32, 32, 32, 32, 32, 28, 28, 22, 16, 12, 12, 9, 9, 3, 1, 24, 24, 24, 24, 24, 24] 32 rigid atoms, others: [36, 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, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 166 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044897 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044897 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044897/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044897 Building REAL250005044898 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044898' /scratch/stefan/7916127/working/building/REAL250005044898 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044898 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044898/0 /scratch/stefan/7916127/working/building/REAL250005044898 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/6 `/scratch/stefan/7916127/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005044898.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044898 none CC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 39, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 39, 39, 28, 28, 7, 1] 83 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]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044898 none CC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 24, 37, 79, 79, 79, 83, 83, 83, 83, 83, 1, 2, 2, 2, 1, 1, 4, 24, 24, 37, 37, 79, 83] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044898 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044898 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044898/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044898 Building REAL250005044899 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044899' /scratch/stefan/7916127/working/building/REAL250005044899 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044899 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044899/0 /scratch/stefan/7916127/working/building/REAL250005044899 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/7 `/scratch/stefan/7916127/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)C(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044899.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044899 none C[NH+](C)C(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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, 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, 27, 27, 27, 27, 27, 27, 27, 17, 17, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 17, 17, 17, 17, 11, 1] 27 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: 99 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044899 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044899 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044899/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044899 Building REAL250005044900 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044900' /scratch/stefan/7916127/working/building/REAL250005044900 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044900 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044900/0 /scratch/stefan/7916127/working/building/REAL250005044900 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/8 `/scratch/stefan/7916127/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C(F)(F)CO)C1=CC(=O)[N-]O1) `REAL250005044900.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044900 none O=C(NCCNC(=O)C(F)(F)CO)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 15, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 537 conformations in input total number of sets (complete confs): 537 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 9, 27, 30, 84, 84, 84, 178, 178, 178, 179, 1, 1, 1, 1, 1, 1, 10, 27, 27, 30, 30, 84, 179, 179, 537, 1] 537 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 1198 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044900 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044900 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044900/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044900 Building REAL250005044901 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044901' /scratch/stefan/7916127/working/building/REAL250005044901 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044901 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044901/0 /scratch/stefan/7916127/working/building/REAL250005044901 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/9 `/scratch/stefan/7916127/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCO)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044901.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044901 none O=C(CCCCO)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 139, 167, 191, 201, 22, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 139, 139, 183, 183, 191, 191, 201, 201, 603, 59, 22, 22, 14, 14, 4, 1] 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]) total number of confs: 1578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044901 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044901 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044901/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044901 Building REAL250005044902 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044902' /scratch/stefan/7916127/working/building/REAL250005044902 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044902 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044902/0 /scratch/stefan/7916127/working/building/REAL250005044902 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/10 `/scratch/stefan/7916127/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NO1) `REAL250005044902.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044902 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NO1 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.2', 'N.2', 'O.3', '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, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [181, 181, 124, 124, 124, 46, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 181, 124, 46, 46, 30, 30, 11, 1, 181] 181 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]) total number of confs: 484 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: REAL250005044902 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NO1 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.2', 'N.2', 'O.3', '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, 1, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 181 conformations in input total number of sets (complete confs): 181 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 60, 108, 175, 175, 175, 181, 181, 181, 181, 181, 1, 1, 1, 2, 2, 2, 9, 60, 60, 108, 108, 175, 181, 1] 181 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 700 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044902 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044902 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044902/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044902 Building REAL250005044903 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044903' /scratch/stefan/7916127/working/building/REAL250005044903 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044903 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044903/0 /scratch/stefan/7916127/working/building/REAL250005044903 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/11 `/scratch/stefan/7916127/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005044903.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044903 none CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 79, 43, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 79, 79, 79, 79, 79, 79, 79, 43, 43, 30, 30, 7, 1, 79] 79 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]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044903 none CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 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, 1, 4, 4, 3, 25, 41, 77, 77, 77, 79, 79, 79, 79, 79, 1, 2, 2, 2, 1, 1, 4, 26, 26, 41, 41, 77, 79, 1] 79 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 290 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044903 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044903 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044903/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044903 Building REAL250005044904 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044904' /scratch/stefan/7916127/working/building/REAL250005044904 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044904 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044904/0 /scratch/stefan/7916127/working/building/REAL250005044904 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/12 `/scratch/stefan/7916127/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CNC(=O)C1)C1=CC(=O)[N-]O1) `REAL250005044904.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044904 none O=C(NCCNC(=O)C1CNC(=O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 45, 110, 110, 110, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 9, 31, 31, 45, 45, 110, 178, 178, 178, 178, 178, 178, 1] 178 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 574 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: REAL250005044904 none O=C(NCCNC(=O)C1CNC(=O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 88, 54, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 169, 178, 178, 178, 178, 178, 169, 88, 88, 54, 54, 10, 1, 1, 1, 1, 1, 1, 178] 178 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 638 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044904 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044904 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044904/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044904 Building REAL250005044905 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044905' /scratch/stefan/7916127/working/building/REAL250005044905 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044905 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044905/0 /scratch/stefan/7916127/working/building/REAL250005044905 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/13 `/scratch/stefan/7916127/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044905.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044905 none O=C(COC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 167, 201, 201, 201, 201, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 167, 167, 73, 27, 27, 16, 16, 4, 1] 201 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]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044905 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044905 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044905/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044905 Building REAL250005044906 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044906' /scratch/stefan/7916127/working/building/REAL250005044906 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044906 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044906/0 /scratch/stefan/7916127/working/building/REAL250005044906 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/14 `/scratch/stefan/7916127/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CNC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005044906.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044906 none O=C(NCCNC(=O)[C@@H]1CNC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 39, 99, 99, 99, 153, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 9, 28, 28, 39, 39, 99, 153, 153, 153, 153, 1] 153 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 509 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: REAL250005044906 none O=C(NCCNC(=O)[C@@H]1CNC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 88, 64, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 144, 153, 153, 153, 153, 153, 144, 88, 88, 64, 64, 12, 1, 1, 1, 1, 153] 153 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 559 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044906 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044906 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044906/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044906 Building REAL250005044907 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044907' /scratch/stefan/7916127/working/building/REAL250005044907 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044907 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044907/0 /scratch/stefan/7916127/working/building/REAL250005044907 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/15 `/scratch/stefan/7916127/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1) `REAL250005044907.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044907 none O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [7, 1, 7, 7, 22, 37, 75, 75, 75, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 7, 22, 22, 37, 37, 75, 107, 107, 1] 107 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005044907 none O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [103, 103, 60, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 103, 107, 107, 107, 107, 107, 103, 60, 60, 42, 42, 12, 1, 1, 107] 107 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044907 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044907 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044907/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044907 Building REAL250005044908 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044908' /scratch/stefan/7916127/working/building/REAL250005044908 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044908 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044908/0 /scratch/stefan/7916127/working/building/REAL250005044908 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/16 `/scratch/stefan/7916127/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005044908.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044908 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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, 123, 123, 123, 94, 94, 94, 41, 26, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 94, 41, 41, 26, 26, 11, 1, 123] 123 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]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044908 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 62, 114, 114, 114, 123, 123, 123, 123, 123, 1, 2, 2, 2, 1, 1, 10, 40, 40, 62, 62, 114, 123, 1] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044908 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044908 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044908/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044908 Building REAL250005044909 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044909' /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005044909 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044909/0 /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/17 `/scratch/stefan/7916127/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044909.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044909 none C[N@@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 7, 1] 17 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: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044909 none C[N@@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 12, 13, 13, 13, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 12, 12, 13, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 32, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005044909/1 /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/18 `/scratch/stefan/7916127/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044909.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005044909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044909/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044909 none C[N@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 6, 1] 16 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: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044909 none C[N@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 12, 13, 13, 13, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 12, 12, 13, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 32, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005044909/2 /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/19 `/scratch/stefan/7916127/working/3D/19' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044909.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005044909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044909/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044909 none CN1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', '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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 86, 86, 86, 43, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 86, 43, 43, 29, 29, 8, 1] 93 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: 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: REAL250005044909 none CN1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', '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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 30, 47, 88, 88, 88, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 47, 47, 88, 93] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044909 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044909 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005044909/1.* 0: /scratch/stefan/7916127/working/building/REAL250005044909/0.* 2: /scratch/stefan/7916127/working/building/REAL250005044909/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044909 Building REAL250005044910 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044910' /scratch/stefan/7916127/working/building/REAL250005044910 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044910 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044910/0 /scratch/stefan/7916127/working/building/REAL250005044910 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/20 `/scratch/stefan/7916127/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CO)CC1)C1=CC(=O)[N-]O1) `REAL250005044910.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044910 none O=C(NCCNC(=O)C1(CO)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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, 6, 20, 32, 89, 89, 89, 173, 201, 173, 173, 1, 1, 1, 1, 1, 1, 6, 20, 20, 32, 32, 89, 201, 201, 603, 173, 173, 173, 173, 1] 603 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 1311 number of broken/clashed sets: 61 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044910 none O=C(NCCNC(=O)C1(CO)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 63, 43, 7, 7, 1, 7, 1, 1, 10, 1, 1, 156, 173, 173, 173, 173, 173, 156, 63, 63, 43, 43, 7, 10, 10, 30, 1, 1, 1, 1, 173] 603 rigid atoms, others: [6, 8, 9, 11, 12, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32]) total number of confs: 619 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044910 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044910 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044910/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044910 Building REAL250005044911 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044911' /scratch/stefan/7916127/working/building/REAL250005044911 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044911 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044911/0 /scratch/stefan/7916127/working/building/REAL250005044911 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/21 `/scratch/stefan/7916127/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044911.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044911 none CCC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 136, 136, 136, 136, 136, 79, 79, 79, 34, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 136, 136, 136, 79, 34, 34, 20, 20, 4, 1] 201 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: 750 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: REAL250005044911 none CCC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 48, 71, 130, 130, 130, 136, 136, 136, 136, 136, 6, 6, 6, 6, 6, 1, 1, 1, 10, 48, 48, 71, 71, 130, 136] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 504 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044911 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044911 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044911/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044911 Building REAL250005044912 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044912' /scratch/stefan/7916127/working/building/REAL250005044912 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044912 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044912/0 /scratch/stefan/7916127/working/building/REAL250005044912 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/22 `/scratch/stefan/7916127/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CCC[C@H]1CF)C1=CC(=O)[N-]O1) `REAL250005044912.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044912 none O=C(NCCNC(=O)[C@@H]1CCC[C@H]1CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 30, 89, 89, 89, 196, 196, 196, 196, 196, 196, 196, 201, 1, 1, 1, 1, 1, 1, 4, 18, 18, 30, 30, 89, 196, 196, 196, 196, 196, 196, 201, 201, 1] 201 rigid atoms, others: [1, 37, 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]) total number of confs: 626 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: REAL250005044912 none O=C(NCCNC(=O)[C@@H]1CCC[C@H]1CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 180, 71, 50, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 180, 196, 196, 196, 196, 196, 182, 71, 71, 50, 50, 10, 1, 1, 1, 1, 1, 1, 7, 7, 196] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37]) total number of confs: 658 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044912 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044912 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044912/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044912 Building REAL250005044913 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044913' /scratch/stefan/7916127/working/building/REAL250005044913 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044913 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044913/0 /scratch/stefan/7916127/working/building/REAL250005044913 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/23 `/scratch/stefan/7916127/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)[C@@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044913.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044913 none CC(C)[C@@H](O)[C@@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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', 'H', '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, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 81, 86, 86, 50, 81, 81, 50, 50, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 258, 81, 81, 81, 50, 21, 21, 14, 14, 4, 1] 258 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: 599 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044913 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044913 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044913/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044913 Building REAL250005044914 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044914' /scratch/stefan/7916127/working/building/REAL250005044914 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044914 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044914/0 /scratch/stefan/7916127/working/building/REAL250005044914 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/24 `/scratch/stefan/7916127/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005044914.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044914 none COC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens need 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, 151, 54, 54, 54, 29, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 195, 195, 201, 201, 201, 151, 151, 54, 29, 29, 18, 18, 4, 1, 195, 195, 195, 195] 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: 761 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: REAL250005044914 none COC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 1, 1, 10, 42, 42, 42, 108, 122, 193, 193, 193, 195, 195, 195, 195, 195, 1, 1, 7, 7, 7, 10, 10, 42, 108, 108, 122, 122, 193, 195, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 35, 33, 34, 18, 19] set([0, 4, 5, 6, 7, 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: 720 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044914 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044914 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044914/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044914 Building REAL250005044915 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044915' /scratch/stefan/7916127/working/building/REAL250005044915 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044915 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044915/0 /scratch/stefan/7916127/working/building/REAL250005044915 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/25 `/scratch/stefan/7916127/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005044915.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044915 none CN1N=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 167, 64, 64, 64, 27, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 167, 167, 64, 27, 27, 18, 18, 4, 1] 201 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]) 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: REAL250005044915 none CN1N=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 37, 37, 37, 93, 116, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 9, 9, 37, 93, 93, 116, 116, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044915 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044915 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044915/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044915 Building REAL250005044916 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044916' /scratch/stefan/7916127/working/building/REAL250005044916 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044916 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044916/0 /scratch/stefan/7916127/working/building/REAL250005044916 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/26 `/scratch/stefan/7916127/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044916.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044916 none O=C(CC1CC1(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 176, 201, 201, 201, 201, 27, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 64, 27, 27, 16, 16, 4, 1] 201 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]) total number of confs: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044916 none O=C(CC1CC1(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 39, 39, 122, 147, 200, 201, 200, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 39, 122, 122, 147, 147, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 777 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044916 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044916 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044916/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044916 Building REAL250005044917 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044917' /scratch/stefan/7916127/working/building/REAL250005044917 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044917 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044917/0 /scratch/stefan/7916127/working/building/REAL250005044917 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/27 `/scratch/stefan/7916127/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)NC=N1)C1=CC(=O)[N-]O1) `REAL250005044917.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044917 none O=C(NCCNC(=O)C1=CC(=O)NC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 22, 33, 69, 69, 69, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 7, 22, 22, 33, 33, 69, 87, 87, 87, 1] 87 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044917 none O=C(NCCNC(=O)C1=CC(=O)NC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [85, 85, 59, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 85, 87, 87, 87, 87, 87, 85, 59, 59, 45, 45, 11, 1, 1, 1, 87] 87 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044917 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044917 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044917/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044917 Building REAL250005044918 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044918' /scratch/stefan/7916127/working/building/REAL250005044918 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044918 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044918/0 /scratch/stefan/7916127/working/building/REAL250005044918 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/28 `/scratch/stefan/7916127/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@H](O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044918.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044918 none CC[C@H](C)[C@H](O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 136, 183, 183, 97, 136, 136, 97, 97, 35, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 183, 408, 97, 35, 35, 23, 23, 4, 1] 603 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: 1261 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044918 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044918 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044918/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044918 Building REAL250005044919 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044919' /scratch/stefan/7916127/working/building/REAL250005044919 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044919 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044919/0 /scratch/stefan/7916127/working/building/REAL250005044919 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/29 `/scratch/stefan/7916127/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]12C[C@H]1[C@H](O)C2)C1=CC(=O)[N-]O1) `REAL250005044919.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044919 none O=C(NCCNC(=O)[C@]12C[C@H]1[C@H](O)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 50, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 30, 30, 50, 50, 109, 201, 201, 603, 201, 201, 1] 603 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: 1120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044919 none O=C(NCCNC(=O)[C@]12C[C@H]1[C@H](O)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 7, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 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: [196, 193, 91, 49, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 196, 91, 91, 49, 49, 7, 1, 1, 6, 1, 1, 201] 603 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 33, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044919 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044919 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044919/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044919 Building REAL250005044920 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044920' /scratch/stefan/7916127/working/building/REAL250005044920 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044920 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044920/0 /scratch/stefan/7916127/working/building/REAL250005044920 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/30 `/scratch/stefan/7916127/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044920.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044920 none CCCOCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 109, 71, 67, 69, 41, 41, 41, 15, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 69, 69, 71, 71, 71, 71, 41, 15, 15, 10, 10, 2, 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: 892 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044920 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044920 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044920/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044920 Building REAL250005044921 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044921' /scratch/stefan/7916127/working/building/REAL250005044921 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044921 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044921/0 /scratch/stefan/7916127/working/building/REAL250005044921 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/31 `/scratch/stefan/7916127/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005044921.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044921 none CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [154, 154, 150, 154, 154, 95, 95, 95, 43, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 150, 154, 95, 43, 43, 30, 30, 7, 1] 154 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]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044921 none CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 81, 144, 146, 144, 154, 154, 154, 154, 154, 1, 2, 2, 2, 1, 1, 10, 52, 52, 81, 81, 146, 154] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044921 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044921 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044921/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044921 Building REAL250005044922 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044922' /scratch/stefan/7916127/working/building/REAL250005044922 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044922 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044922/0 /scratch/stefan/7916127/working/building/REAL250005044922 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/32 `/scratch/stefan/7916127/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCF)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044922.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044922 none O=C(CCCCCF)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 15, 8, 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: [6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 132, 151, 179, 179, 197, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 132, 132, 169, 169, 178, 178, 201, 201, 193, 193, 37, 25, 25, 16, 16, 4, 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: 1093 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044922 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044922 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044922/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044922 Building REAL250005044923 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044923' /scratch/stefan/7916127/working/building/REAL250005044923 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044923 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044923/0 /scratch/stefan/7916127/working/building/REAL250005044923 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/33 `/scratch/stefan/7916127/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2(CC2F)C1)C1=CC(=O)[N-]O1) `REAL250005044923.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044923 none O=C(NCCNC(=O)C1CC2(CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens 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, 8, 33, 49, 118, 118, 118, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 33, 33, 49, 49, 118, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 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]) total number of confs: 646 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: REAL250005044923 none O=C(NCCNC(=O)C1CC2(CC2F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 111, 67, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 111, 111, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 749 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044923 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044923 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044923/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044923 Building REAL250005044924 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044924' /scratch/stefan/7916127/working/building/REAL250005044924 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044924 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044924/0 /scratch/stefan/7916127/working/building/REAL250005044924 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/34 `/scratch/stefan/7916127/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044924.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044924 none COC(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 190, 108, 190, 108, 108, 40, 25, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 190, 108, 40, 40, 25, 25, 4, 1] 201 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]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044924 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044924 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044924/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044924 Building REAL250005044925 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044925' /scratch/stefan/7916127/working/building/REAL250005044925 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044925 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044925/0 /scratch/stefan/7916127/working/building/REAL250005044925 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/35 `/scratch/stefan/7916127/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)ON=C1) `REAL250005044925.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044925 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)ON=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'N.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 144, 144, 119, 119, 119, 43, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 144, 144, 144, 201, 201, 201, 201, 201, 119, 43, 43, 26, 26, 4, 1, 144] 201 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]) total number of confs: 751 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044925 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)ON=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'N.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 10, 10, 10, 38, 59, 140, 140, 140, 144, 144, 144, 144, 144, 1, 1, 1, 6, 6, 6, 6, 6, 10, 38, 38, 59, 59, 140, 144, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044925 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044925 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044925/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044925 Building REAL250005044926 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044926' /scratch/stefan/7916127/working/building/REAL250005044926 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044926 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044926/0 /scratch/stefan/7916127/working/building/REAL250005044926 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/36 `/scratch/stefan/7916127/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044926.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044926 none O=C(COC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 117, 201, 201, 201, 201, 201, 25, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 117, 117, 201, 201, 55, 25, 25, 18, 18, 4, 1] 201 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]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044926 none O=C(COC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 12, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 17, 3, 1, 1, 1, 1, 1, 1, 68, 68, 146, 153, 201, 201, 201, 201, 201, 201, 201, 201, 17, 17, 1, 1, 68, 146, 146, 153, 153, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044926 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044926 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044926/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044926 Building REAL250005044927 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044927' /scratch/stefan/7916127/working/building/REAL250005044927 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044927 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044927/0 /scratch/stefan/7916127/working/building/REAL250005044927 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/37 `/scratch/stefan/7916127/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1C) `REAL250005044927.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044927 none CC1=COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', '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.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 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: [155, 155, 155, 155, 125, 125, 125, 66, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 125, 66, 66, 36, 36, 9, 1, 155, 155, 155] 155 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: 502 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044927 none CC1=COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', '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.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 87, 145, 145, 145, 155, 155, 155, 155, 155, 1, 1, 2, 2, 2, 1, 9, 47, 47, 87, 87, 145, 155, 2, 2, 2] 155 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044927 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044927 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044927/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044927 Building REAL250005044928 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044928' /scratch/stefan/7916127/working/building/REAL250005044928 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044928 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044928/0 /scratch/stefan/7916127/working/building/REAL250005044928 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/38 `/scratch/stefan/7916127/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044928.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044928 none O=C(CC1=CN=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 148, 201, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 148, 148, 201, 201, 201, 71, 23, 23, 14, 14, 4, 1] 201 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: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044928 none O=C(CC1=CN=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 7, 1, 1, 1, 1, 1, 1, 1, 29, 29, 93, 128, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 29, 93, 93, 128, 128, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044928 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044928 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044928/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044928 Building REAL250005044929 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044929' /scratch/stefan/7916127/working/building/REAL250005044929 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044929 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044929/0 /scratch/stefan/7916127/working/building/REAL250005044929 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/39 `/scratch/stefan/7916127/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1OCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044929.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044929 none CCC1OCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 112, 92, 92, 93, 41, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 112, 93, 41, 41, 30, 30, 11, 1] 112 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: 383 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: REAL250005044929 none CCC1OCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 18, 32, 101, 101, 101, 112, 112, 112, 112, 112, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 18, 18, 32, 32, 101, 112] 112 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 353 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044929 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044929 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044929/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044929 Building REAL250005044930 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044930' /scratch/stefan/7916127/working/building/REAL250005044930 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044930 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044930/0 /scratch/stefan/7916127/working/building/REAL250005044930 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/40 `/scratch/stefan/7916127/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C12CC1CC2)C1=CC(=O)[N-]O1) `REAL250005044930.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044930 none O=C(NCCNC(=O)C12CC1CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 48, 98, 98, 98, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 30, 30, 48, 48, 98, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044930 none O=C(NCCNC(=O)C12CC1CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 89, 49, 7, 7, 1, 7, 1, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 190, 89, 89, 49, 49, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044930 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044930 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044930/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044930 Building REAL250005044931 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044931' /scratch/stefan/7916127/working/building/REAL250005044931 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044931 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044931/0 /scratch/stefan/7916127/working/building/REAL250005044931 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/41 `/scratch/stefan/7916127/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044931.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044931 none CCCC(C)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.3', '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', 'H', '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, 5, 1, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 130, 130, 130, 68, 68, 68, 24, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 130, 130, 130, 130, 68, 24, 24, 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: 803 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044931 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044931 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044931/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044931 Building REAL250005044932 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044932' /scratch/stefan/7916127/working/building/REAL250005044932 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044932 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044932/0 /scratch/stefan/7916127/working/building/REAL250005044932 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/42 `/scratch/stefan/7916127/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@H](C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044932.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044932 none C=C[C@H](C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 201, 200, 63, 63, 63, 30, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 153, 153, 63, 30, 30, 20, 20, 4, 1] 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]) total number of confs: 865 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044932 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044932 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044932/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044932 Building REAL250005044933 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044933' /scratch/stefan/7916127/working/building/REAL250005044933 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044933 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044933/0 /scratch/stefan/7916127/working/building/REAL250005044933 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/43 `/scratch/stefan/7916127/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044933.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044933 none O=C(C=CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 92, 92, 169, 169, 201, 201, 40, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 92, 40, 40, 25, 25, 4, 1] 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]) total number of confs: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044933 none O=C(C=CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 10, 10, 1, 1, 1, 1, 47, 47, 113, 144, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 47, 113, 113, 144, 144, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 21, 22, 23, 24, 25] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 775 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044933 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044933 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044933/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044933 Building REAL250005044934 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044934' /scratch/stefan/7916127/working/building/REAL250005044934 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044934 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044934/0 /scratch/stefan/7916127/working/building/REAL250005044934 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/44 `/scratch/stefan/7916127/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C12CCC(CC1)O2)C1=CC(=O)[N-]O1) `REAL250005044934.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044934 none O=C(NCCNC(=O)C12CCC(CC1)O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 8, 28, 37, 94, 94, 94, 159, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 9, 28, 28, 37, 37, 94, 159, 159, 159, 159, 159, 159, 159, 159, 159, 1] 159 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: 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: REAL250005044934 none O=C(NCCNC(=O)C12CCC(CC1)O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 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 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [154, 153, 97, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 154, 159, 159, 159, 159, 159, 154, 97, 97, 69, 69, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 159] 159 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044934 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044934 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044934/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044934 Building REAL250005044935 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044935' /scratch/stefan/7916127/working/building/REAL250005044935 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044935 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044935/0 /scratch/stefan/7916127/working/building/REAL250005044935 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/45 `/scratch/stefan/7916127/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044935.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044935 none CC=C(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 70, 162, 201, 70, 70, 28, 19, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 201, 201, 201, 201, 201, 70, 28, 28, 19, 19, 4, 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: 747 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044935 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044935 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044935/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044935 Building REAL250005044936 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044936' /scratch/stefan/7916127/working/building/REAL250005044936 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005044936 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044936/0 /scratch/stefan/7916127/working/building/REAL250005044936 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/46 `/scratch/stefan/7916127/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(F)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1) `REAL250005044936.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044936 none CC1=C(F)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', '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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 75, 75, 75, 39, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 75, 39, 39, 24, 24, 7, 1, 87] 87 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]) total number of confs: 290 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044936 none CC1=C(F)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'F', '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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 15, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 7, 7, 7, 29, 47, 85, 85, 85, 87, 87, 87, 87, 87, 1, 1, 2, 2, 2, 7, 29, 29, 47, 47, 85, 87, 1] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044936 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005044936/1 /scratch/stefan/7916127/working/building/REAL250005044936 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/47 `/scratch/stefan/7916127/working/3D/47' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1F) `REAL250005044936.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005044936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044936/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044936 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 95, 87, 87, 87, 39, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 87, 39, 39, 26, 26, 7, 1] 95 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]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044936 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 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, 6, 27, 43, 89, 89, 89, 95, 95, 95, 95, 95, 1, 1, 2, 2, 2, 1, 6, 26, 26, 43, 43, 89, 95] 95 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044936 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044936 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005044936/1.* 0: /scratch/stefan/7916127/working/building/REAL250005044936/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044936 Building REAL250005044937 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044937' /scratch/stefan/7916127/working/building/REAL250005044937 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044937 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044937/0 /scratch/stefan/7916127/working/building/REAL250005044937 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/48 `/scratch/stefan/7916127/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC12CC(C1)C2)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044937.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044937 none O=C(CC12CC(C1)C2)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 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: [76, 76, 76, 140, 142, 142, 142, 142, 41, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 142, 142, 142, 142, 142, 142, 142, 142, 142, 76, 41, 41, 24, 24, 4, 1] 142 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: 590 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044937 none O=C(CC12CC(C1)C2)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 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: [36, 9, 1, 1, 1, 1, 1, 1, 36, 36, 83, 92, 142, 142, 142, 142, 142, 142, 142, 142, 9, 9, 1, 1, 1, 1, 1, 1, 1, 36, 83, 83, 92, 92, 142, 142] 142 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044937 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044937 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044937/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044937 Building REAL250005044938 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044938' /scratch/stefan/7916127/working/building/REAL250005044938 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044938 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044938/0 /scratch/stefan/7916127/working/building/REAL250005044938 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/49 `/scratch/stefan/7916127/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(CC#C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044938.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044938 none C#CCC(CC#C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 103, 44, 103, 157, 157, 44, 44, 19, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 160, 160, 160, 103, 157, 157, 157, 44, 19, 19, 13, 13, 4, 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: 1010 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044938 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044938 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044938/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044938 Building REAL250005044939 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044939' /scratch/stefan/7916127/working/building/REAL250005044939 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044939 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044939/0 /scratch/stefan/7916127/working/building/REAL250005044939 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/50 `/scratch/stefan/7916127/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)O) `REAL250005044939.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044939 none CCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)O 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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 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, 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: [121, 114, 68, 68, 68, 27, 19, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 114, 135, 138, 123, 123, 123, 123, 123, 114, 68, 27, 27, 19, 19, 5, 1, 138, 138, 138, 138, 414] 426 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]) total number of confs: 1090 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044939 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044939 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044939/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044939 Building REAL250005044940 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044940' /scratch/stefan/7916127/working/building/REAL250005044940 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044940 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044940/0 /scratch/stefan/7916127/working/building/REAL250005044940 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/51 `/scratch/stefan/7916127/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044940.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044940 none CCC(NC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', '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', '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, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 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] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [124, 113, 77, 113, 125, 125, 125, 77, 77, 29, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 113, 125, 125, 125, 77, 29, 29, 17, 17, 4, 1] 129 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: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044940 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044940 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044940/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044940 Building REAL250005044941 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044941' /scratch/stefan/7916127/working/building/REAL250005044941 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044941 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044941/0 /scratch/stefan/7916127/working/building/REAL250005044941 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/52 `/scratch/stefan/7916127/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(CO)=C1) `REAL250005044941.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044941 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(CO)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 5, 12, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 4, 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: [5, 1, 5, 5, 29, 45, 149, 149, 149, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 8, 1, 5, 29, 29, 45, 45, 149, 178, 1, 8, 8, 24, 1] 603 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 20, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044941 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(CO)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'C.3', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 5, 12, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 7, 4, 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: [93, 93, 41, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 93, 178, 178, 178, 178, 201, 178, 93, 41, 41, 30, 30, 9, 1, 178, 201, 201, 603, 178] 603 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]) total number of confs: 1200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044941 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044941 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044941/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044941 Building REAL250005044942 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044942' /scratch/stefan/7916127/working/building/REAL250005044942 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044942 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044942/0 /scratch/stefan/7916127/working/building/REAL250005044942 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/53 `/scratch/stefan/7916127/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044942.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044942 none C=CC(C)(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 546 conformations in input total number of sets (complete confs): 546 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 127, 182, 182, 127, 129, 47, 29, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 182, 546, 129, 47, 47, 29, 29, 8, 1] 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]) total number of confs: 1249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044942 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044942 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044942/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044942 Building REAL250005044943 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044943' /scratch/stefan/7916127/working/building/REAL250005044943 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044943 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044943/0 /scratch/stefan/7916127/working/building/REAL250005044943 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/54 `/scratch/stefan/7916127/working/3D/54' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1(O)CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044943.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044943 none O=C(CCC1(O)CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 12, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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, 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, 130, 127, 201, 201, 201, 201, 30, 20, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 131, 131, 152, 153, 603, 201, 201, 201, 201, 201, 201, 56, 30, 30, 20, 20, 8, 1] 603 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: 1483 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: REAL250005044943 none O=C(CCC1(O)CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 12, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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, 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: [52, 14, 7, 1, 1, 1, 1, 1, 1, 52, 52, 141, 167, 197, 197, 197, 201, 201, 201, 201, 201, 14, 14, 7, 7, 6, 1, 1, 1, 1, 1, 1, 52, 141, 141, 167, 167, 197, 201] 603 rigid atoms, others: [3, 4, 5, 6, 7, 8, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 808 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044943 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044943 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044943/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044943 Building REAL250005044944 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044944' /scratch/stefan/7916127/working/building/REAL250005044944 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044944 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044944/0 /scratch/stefan/7916127/working/building/REAL250005044944 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/55 `/scratch/stefan/7916127/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044944.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044944 none CCC(C)(CO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 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, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [166, 152, 79, 152, 151, 196, 79, 79, 29, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 152, 152, 152, 196, 196, 588, 79, 29, 29, 18, 18, 4, 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: 1682 number of broken/clashed sets: 86 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044944 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044944 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044944/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044944 Building REAL250005044945 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044945' /scratch/stefan/7916127/working/building/REAL250005044945 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005044945 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044945/0 /scratch/stefan/7916127/working/building/REAL250005044945 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/56 `/scratch/stefan/7916127/working/3D/56' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005044945.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044945 none C[NH+](C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 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', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 13, 13, 13, 11, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 13, 11, 11, 11, 11, 8, 1, 15, 15, 15, 15] 15 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: 45 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: REAL250005044945 none C[NH+](C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 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', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 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, 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: [2, 1, 2, 2, 1, 1, 3, 3, 3, 9, 11, 11, 11, 11, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 2, 2, 2, 3, 9, 9, 11, 11, 11, 15, 1, 1, 1, 1] 15 rigid atoms, others: [1, 34, 35, 4, 5, 19, 20, 36, 37] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044945 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005044945/1 /scratch/stefan/7916127/working/building/REAL250005044945 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/57 `/scratch/stefan/7916127/working/3D/57' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005044945.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005044945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044945/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044945 none CN(C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 83, 83, 83, 44, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112, 112, 112, 83, 44, 44, 30, 30, 9, 1, 112, 112, 112, 112] 112 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]) total number of confs: 390 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: REAL250005044945 none CN(C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 6, 25, 43, 106, 106, 106, 112, 112, 112, 112, 112, 1, 1, 3, 3, 3, 3, 3, 3, 6, 25, 25, 43, 43, 106, 112, 1, 1, 1, 1] 112 rigid atoms, others: [1, 34, 3, 4, 35, 33, 18, 19, 36] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 382 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044945 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044945 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005044945/1.* 0: /scratch/stefan/7916127/working/building/REAL250005044945/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044945 Building REAL250005044946 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044946' /scratch/stefan/7916127/working/building/REAL250005044946 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044946 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044946/0 /scratch/stefan/7916127/working/building/REAL250005044946 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/58 `/scratch/stefan/7916127/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC[NH+]1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044946.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044946 none O=C(CC[NH+]1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 1, 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, 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: [32, 32, 32, 39, 39, 48, 48, 48, 48, 48, 21, 21, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 32, 21, 21, 21, 21, 11, 1] 48 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: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044946 none O=C(CC[NH+]1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 1, 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, 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: [24, 7, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 38, 39, 39, 39, 39, 48, 48, 48, 48, 48, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 39, 39, 39, 39, 39, 48] 48 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044946 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044946 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044946/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044946 Building REAL250005044947 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044947' /scratch/stefan/7916127/working/building/REAL250005044947 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044947 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044947/0 /scratch/stefan/7916127/working/building/REAL250005044947 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/59 `/scratch/stefan/7916127/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044947.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044947 none CC1(C)CC1CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 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, 151, 129, 40, 40, 40, 21, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 130, 130, 40, 21, 21, 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: 896 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044947 none CC1(C)CC1CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 5, 11, 45, 45, 45, 126, 150, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 11, 11, 45, 127, 127, 151, 151, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044947 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044947 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044947/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044947 Building REAL250005044948 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044948' /scratch/stefan/7916127/working/building/REAL250005044948 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044948 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044948/0 /scratch/stefan/7916127/working/building/REAL250005044948 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/60 `/scratch/stefan/7916127/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044948.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044948 none O=C(C=CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 156, 156, 201, 201, 201, 201, 33, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 201, 201, 201, 201, 73, 33, 33, 22, 22, 4, 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: 662 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044948 none O=C(C=CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 32, 32, 91, 123, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 32, 91, 91, 123, 123, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 755 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044948 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044948 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044948/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044948 Building REAL250005044949 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044949' /scratch/stefan/7916127/working/building/REAL250005044949 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044949 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044949/0 /scratch/stefan/7916127/working/building/REAL250005044949 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/61 `/scratch/stefan/7916127/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC12CC(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)(C1)OC2) `REAL250005044949.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044949 none CC12CC(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 97, 97, 99, 47, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 144, 144, 144, 144, 144, 144, 144, 144, 99, 47, 47, 30, 30, 9, 1, 144, 144, 144, 144] 145 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]) 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: REAL250005044949 none CC12CC(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)(C1)OC2 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 57, 85, 139, 141, 139, 144, 144, 144, 144, 144, 1, 1, 1, 2, 2, 2, 1, 1, 12, 57, 57, 85, 85, 141, 144, 1, 1, 1, 1] 145 rigid atoms, others: [0, 1, 2, 3, 4, 35, 33, 34, 18, 19, 20, 24, 25, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 553 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044949 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044949 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044949/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044949 Building REAL250005044950 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044950' /scratch/stefan/7916127/working/building/REAL250005044950 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044950 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044950/0 /scratch/stefan/7916127/working/building/REAL250005044950 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/62 `/scratch/stefan/7916127/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(O)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005044950.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044950 none C#CC1(O)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 110, 110, 110, 44, 29, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 603, 201, 201, 201, 110, 44, 44, 29, 29, 8, 1, 201, 201] 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]) total number of confs: 1255 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: REAL250005044950 none C#CC1(O)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 69, 111, 192, 193, 192, 201, 201, 201, 201, 201, 1, 1, 6, 1, 1, 1, 13, 69, 69, 111, 111, 193, 201, 1, 1] 603 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 20, 21, 23, 24, 25] set([32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 26, 27, 28, 29, 30, 31]) total number of confs: 758 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044950 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044950 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044950/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044950 Building REAL250005044951 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044951' /scratch/stefan/7916127/working/building/REAL250005044951 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044951 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044951/0 /scratch/stefan/7916127/working/building/REAL250005044951 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/63 `/scratch/stefan/7916127/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005044951.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044951 none CC1=C(C)NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 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, 114, 114, 85, 85, 85, 37, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 114, 114, 85, 37, 37, 22, 22, 9, 1, 114] 114 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]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044951 none CC1=C(C)NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 37, 58, 108, 108, 108, 114, 114, 114, 114, 114, 1, 2, 2, 2, 2, 2, 2, 1, 10, 37, 37, 58, 58, 108, 114, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 430 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044951 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044951 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044951/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044951 Building REAL250005044952 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044952' /scratch/stefan/7916127/working/building/REAL250005044952 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044952 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044952/0 /scratch/stefan/7916127/working/building/REAL250005044952 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/64 `/scratch/stefan/7916127/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2CCCC21)C1=CC(=O)[N-]O1) `REAL250005044952.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044952 none O=C(NCCNC(=O)C1CC2CCCC21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 35, 60, 142, 142, 142, 193, 193, 193, 193, 193, 193, 1, 1, 1, 1, 1, 1, 11, 35, 35, 60, 60, 142, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 193, 1] 193 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: 662 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044952 none O=C(NCCNC(=O)C1CC2CCCC21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [172, 172, 80, 44, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 172, 193, 193, 193, 193, 193, 172, 80, 80, 44, 44, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 193] 193 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 652 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044952 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044952 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044952/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044952 Building REAL250005044953 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044953' /scratch/stefan/7916127/working/building/REAL250005044953 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044953 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044953/0 /scratch/stefan/7916127/working/building/REAL250005044953 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/65 `/scratch/stefan/7916127/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C12CC(C1)CO2)C1=CC(=O)[N-]O1) `REAL250005044953.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044953 none O=C(NCCNC(=O)C12CC(C1)CO2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 28, 40, 89, 89, 89, 151, 151, 151, 151, 151, 1, 1, 1, 1, 1, 1, 8, 28, 28, 40, 40, 89, 151, 151, 151, 151, 151, 151, 151, 1] 151 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044953 none O=C(NCCNC(=O)C12CC(C1)CO2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [146, 145, 88, 67, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 145, 151, 151, 151, 151, 151, 146, 88, 88, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 151] 151 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044953 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044953 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044953/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044953 Building REAL250005044954 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044954' /scratch/stefan/7916127/working/building/REAL250005044954 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044954 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044954/0 /scratch/stefan/7916127/working/building/REAL250005044954 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/66 `/scratch/stefan/7916127/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(O)C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044954.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044954 none O=C(CC1CCC(O)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 172, 201, 201, 201, 201, 201, 31, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 172, 172, 201, 201, 201, 201, 201, 201, 603, 201, 201, 59, 31, 31, 22, 22, 4, 1] 603 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: 1349 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044954 none O=C(CC1CCC(O)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [34, 7, 1, 1, 1, 1, 1, 1, 1, 34, 34, 114, 131, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 6, 1, 1, 34, 114, 114, 131, 131, 201, 201] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044954 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044954 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044954/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044954 Building REAL250005044955 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044955' /scratch/stefan/7916127/working/building/REAL250005044955 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044955 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044955/0 /scratch/stefan/7916127/working/building/REAL250005044955 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/67 `/scratch/stefan/7916127/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)O) `REAL250005044955.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044955 none C[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 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] 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: [98, 71, 98, 71, 71, 32, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 98, 111, 100, 111, 98, 98, 98, 71, 32, 32, 22, 22, 7, 1, 111, 111, 111, 111, 111, 111, 333] 333 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]) total number of confs: 847 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044955 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044955 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044955/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044955 Building REAL250005044956 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044956' /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005044956 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044956/0 /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/68 `/scratch/stefan/7916127/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005044956.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044956 none C[N@@H+]1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 18, 18, 18, 10, 10, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 10, 10, 10, 10, 8, 1, 21, 21] 21 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: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044956 none C[N@@H+]1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 14, 14, 14, 14, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 13, 13, 14, 14, 14, 21, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 25, 26, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005044956/1 /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/69 `/scratch/stefan/7916127/working/3D/69' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005044956.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005044956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044956/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044956 none C[N@H+]1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 18, 18, 18, 10, 10, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 10, 10, 10, 10, 9, 1, 21, 21] 21 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: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044956 none C[N@H+]1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 14, 14, 14, 14, 21, 21, 21, 21, 21, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 13, 13, 14, 14, 14, 21, 1, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 25, 26, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005044956/2 /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/70 `/scratch/stefan/7916127/working/3D/70' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2) `REAL250005044956.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005044956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044956/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044956 none CN1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 106, 106, 106, 52, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 139, 139, 139, 106, 52, 52, 34, 34, 9, 1, 139, 139] 139 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]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044956 none CN1CC2CC1(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C2 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 44, 76, 133, 133, 133, 139, 139, 139, 139, 139, 1, 2, 2, 2, 1, 1, 1, 1, 1, 9, 44, 44, 76, 76, 133, 139, 1, 1] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25, 26, 27, 28, 37, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 506 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044956 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044956 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005044956/1.* 0: /scratch/stefan/7916127/working/building/REAL250005044956/0.* 2: /scratch/stefan/7916127/working/building/REAL250005044956/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044956 Building REAL250005044957 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044957' /scratch/stefan/7916127/working/building/REAL250005044957 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044957 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044957/0 /scratch/stefan/7916127/working/building/REAL250005044957 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/71 `/scratch/stefan/7916127/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044957.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044957 none CN1N=NC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 167, 89, 89, 89, 25, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 167, 167, 89, 25, 25, 17, 17, 4, 1] 201 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]) total number of confs: 673 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044957 none CN1N=NC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 25, 25, 25, 89, 107, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 5, 5, 25, 89, 89, 107, 107, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044957 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044957 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044957/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044957 Building REAL250005044958 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044958' /scratch/stefan/7916127/working/building/REAL250005044958 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044958 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044958/0 /scratch/stefan/7916127/working/building/REAL250005044958 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/72 `/scratch/stefan/7916127/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C12CC(C1)OC2)C1=CC(=O)[N-]O1) `REAL250005044958.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044958 none O=C(NCCNC(=O)C12CC(C1)OC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 39, 69, 69, 69, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 26, 26, 39, 39, 69, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044958 none O=C(NCCNC(=O)C12CC(C1)OC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 191, 88, 44, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 191, 201, 201, 201, 201, 201, 191, 88, 88, 44, 44, 7, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 716 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044958 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044958 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044958/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044958 Building REAL250005044959 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044959' /scratch/stefan/7916127/working/building/REAL250005044959 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044959 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044959/0 /scratch/stefan/7916127/working/building/REAL250005044959 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/73 `/scratch/stefan/7916127/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044959.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044959 none CC(O)C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 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 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 86, 62, 62, 62, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 258, 86, 86, 86, 86, 62, 30, 30, 19, 19, 4, 1] 258 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: 555 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: REAL250005044959 none CC(O)C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 6, 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 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 6, 29, 48, 86, 86, 86, 86, 86, 86, 86, 86, 2, 2, 2, 2, 6, 1, 1, 1, 1, 6, 29, 29, 48, 48, 86, 86] 258 rigid atoms, others: [1, 3, 4, 5, 6, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 340 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044959 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044959 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044959/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044959 Building REAL250005044960 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044960' /scratch/stefan/7916127/working/building/REAL250005044960 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044960 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044960/0 /scratch/stefan/7916127/working/building/REAL250005044960 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/74 `/scratch/stefan/7916127/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@]2(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)C[C@@H]12) `REAL250005044960.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044960 none C[C@@H]1C[C@@]2(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 97, 97, 97, 45, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 97, 45, 45, 29, 29, 7, 1, 201, 201] 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: 485 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044960 none C[C@@H]1C[C@@]2(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)C[C@@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 48, 89, 194, 197, 194, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 48, 48, 89, 89, 197, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044960 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044960 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044960/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044960 Building REAL250005044961 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044961' /scratch/stefan/7916127/working/building/REAL250005044961 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044961 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044961/0 /scratch/stefan/7916127/working/building/REAL250005044961 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/75 `/scratch/stefan/7916127/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CO1) `REAL250005044961.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044961 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 196, 123, 123, 123, 48, 32, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 196, 123, 48, 48, 32, 32, 10, 1, 196, 196] 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, 37, 38]) total number of confs: 630 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: REAL250005044961 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 61, 98, 189, 189, 189, 196, 196, 196, 196, 196, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 11, 61, 61, 98, 98, 189, 196, 1, 1] 196 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 19, 20, 27, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 715 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044961 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044961 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044961/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044961 Building REAL250005044962 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044962' /scratch/stefan/7916127/working/building/REAL250005044962 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044962 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044962/0 /scratch/stefan/7916127/working/building/REAL250005044962 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/76 `/scratch/stefan/7916127/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044962.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044962 none O=C(CN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 170, 201, 201, 201, 201, 40, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 108, 40, 40, 25, 25, 4, 1] 201 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]) total number of confs: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044962 none O=C(CN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 35, 35, 97, 134, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 35, 97, 97, 134, 134, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044962 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044962 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044962/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044962 Building REAL250005044963 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044963' /scratch/stefan/7916127/working/building/REAL250005044963 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044963 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044963/0 /scratch/stefan/7916127/working/building/REAL250005044963 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/77 `/scratch/stefan/7916127/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044963.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044963 none CN(C)C(=O)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 201, 150, 92, 92, 92, 33, 26, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 150, 150, 92, 33, 33, 26, 26, 10, 1] 201 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: 638 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044963 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044963 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044963/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044963 Building REAL250005044964 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044964' /scratch/stefan/7916127/working/building/REAL250005044964 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044964 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044964/0 /scratch/stefan/7916127/working/building/REAL250005044964 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/78 `/scratch/stefan/7916127/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC(=O)O1)C1=CC(=O)[N-]O1) `REAL250005044964.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044964 none O=C(NCCNC(=O)C1=CC=CC(=O)O1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 25, 37, 98, 98, 98, 154, 152, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 9, 25, 25, 37, 37, 98, 154, 154, 154, 1] 154 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044964 none O=C(NCCNC(=O)C1=CC=CC(=O)O1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 5, 3, 7, 7, 7, 3, 7, 3, 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: [149, 149, 82, 56, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 149, 154, 154, 154, 154, 154, 149, 82, 82, 56, 56, 11, 1, 1, 1, 154] 154 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044964 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044964 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044964/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044964 Building REAL250005044965 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044965' /scratch/stefan/7916127/working/building/REAL250005044965 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044965 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044965/0 /scratch/stefan/7916127/working/building/REAL250005044965 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/79 `/scratch/stefan/7916127/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C#CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005044965.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044965 none CC1(C#CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'C.1', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 37, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 37, 37, 22, 22, 7, 1, 61, 61, 61, 61] 61 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: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044965 none CC1(C#CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.1', 'C.1', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 23, 55, 55, 55, 61, 61, 61, 61, 61, 1, 1, 2, 2, 2, 1, 9, 9, 23, 23, 55, 61, 1, 1, 1, 1] 61 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 32, 23, 33, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044965 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044965 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044965/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044965 Building REAL250005044966 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044966' /scratch/stefan/7916127/working/building/REAL250005044966 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044966 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044966/0 /scratch/stefan/7916127/working/building/REAL250005044966 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/80 `/scratch/stefan/7916127/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005044966.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044966 none C=CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 152, 61, 61, 61, 29, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 152, 152, 61, 29, 29, 20, 20, 4, 1, 201, 201, 201, 201, 201, 201] 201 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: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044966 none C=CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 7, 27, 27, 27, 93, 113, 192, 194, 192, 201, 201, 201, 201, 201, 1, 1, 1, 6, 6, 6, 7, 7, 27, 93, 93, 113, 113, 194, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([0, 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, 32]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044966 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044966 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044966/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044966 Building REAL250005044967 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044967' /scratch/stefan/7916127/working/building/REAL250005044967 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044967 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044967/0 /scratch/stefan/7916127/working/building/REAL250005044967 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/81 `/scratch/stefan/7916127/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CN=C1) `REAL250005044967.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044967 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CN=C1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 46, 46, 46, 116, 129, 200, 201, 200, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 13, 13, 12, 46, 116, 116, 129, 129, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 741 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044967 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CN=C1 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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 8, 1, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 55, 55, 55, 24, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 125, 125, 125, 125, 55, 24, 24, 16, 16, 4, 1, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044967 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044967 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044967/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044967 Building REAL250005044968 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044968' /scratch/stefan/7916127/working/building/REAL250005044968 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044968 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044968/0 /scratch/stefan/7916127/working/building/REAL250005044968 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/82 `/scratch/stefan/7916127/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CNC1=O)C1=CC(=O)[N-]O1) `REAL250005044968.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044968 none O=C(NCCNC(=O)C1=CC=CNC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 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: [8, 1, 8, 8, 31, 45, 104, 104, 104, 157, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 8, 31, 31, 45, 45, 104, 157, 157, 157, 157, 1] 157 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044968 none O=C(NCCNC(=O)C1=CC=CNC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 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: [152, 152, 97, 66, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 152, 157, 157, 157, 157, 157, 152, 97, 97, 66, 66, 12, 1, 1, 1, 1, 157] 157 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 606 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044968 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044968 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044968/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044968 Building REAL250005044969 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044969' /scratch/stefan/7916127/working/building/REAL250005044969 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044969 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044969/0 /scratch/stefan/7916127/working/building/REAL250005044969 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/83 `/scratch/stefan/7916127/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044969.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044969 none O=C(CSC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 14, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 104, 191, 201, 201, 20, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 106, 106, 201, 38, 20, 20, 12, 12, 4, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044969 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044969 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044969/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044969 Building REAL250005044970 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044970' /scratch/stefan/7916127/working/building/REAL250005044970 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044970 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044970/0 /scratch/stefan/7916127/working/building/REAL250005044970 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/84 `/scratch/stefan/7916127/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005044970.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044970 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 113, 113, 113, 44, 26, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 175, 175, 175, 175, 175, 175, 113, 44, 44, 26, 26, 11, 1, 175, 175, 175, 175] 175 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: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044970 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 32, 59, 155, 157, 157, 175, 175, 175, 175, 175, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 32, 32, 59, 59, 157, 175, 1, 1, 1, 1] 175 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 39, 40, 19, 20, 24, 25, 26, 27, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 576 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044970 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044970 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044970/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044970 Building REAL250005044971 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044971' /scratch/stefan/7916127/working/building/REAL250005044971 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044971 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044971/0 /scratch/stefan/7916127/working/building/REAL250005044971 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/85 `/scratch/stefan/7916127/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC=[N+]1[O-])C1=CC(=O)[N-]O1) `REAL250005044971.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044971 none O=C(NCCNC(=O)C1=CC=CC=[N+]1[O-])C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 22, 31, 78, 78, 78, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 8, 22, 22, 31, 31, 78, 111, 111, 111, 111, 1] 111 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 306 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044971 none O=C(NCCNC(=O)C1=CC=CC=[N+]1[O-])C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 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, 67, 57, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 67, 67, 57, 57, 11, 1, 1, 1, 1, 111] 111 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044971 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044971 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044971/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044971 Building REAL250005044972 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044972' /scratch/stefan/7916127/working/building/REAL250005044972 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044972 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044972/0 /scratch/stefan/7916127/working/building/REAL250005044972 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/86 `/scratch/stefan/7916127/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCC1) `REAL250005044972.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044972 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 6, 21, 33, 58, 58, 58, 62, 62, 62, 62, 62, 1, 1, 1, 1, 6, 21, 21, 33, 33, 58, 62, 1, 1, 1, 1, 1] 62 rigid atoms, others: [1, 14, 15, 16, 17, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 227 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044972 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 38, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 62, 38, 38, 24, 24, 7, 1, 62, 62, 62, 62, 62] 62 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 24] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044972 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044972 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044972/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044972 Building REAL250005044973 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044973' /scratch/stefan/7916127/working/building/REAL250005044973 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044973 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044973/0 /scratch/stefan/7916127/working/building/REAL250005044973 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/87 `/scratch/stefan/7916127/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(F)O1) `REAL250005044973.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044973 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 15, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 7, 32, 50, 86, 86, 86, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 8, 32, 32, 50, 50, 86, 94, 1, 1] 94 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 339 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044973 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(F)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'F', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 15, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 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: [81, 81, 40, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 94, 94, 94, 94, 94, 81, 40, 40, 26, 26, 9, 1, 94, 94] 94 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]) total number of confs: 300 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044973 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044973 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044973/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044973 Building REAL250005044974 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044974' /scratch/stefan/7916127/working/building/REAL250005044974 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044974 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044974/0 /scratch/stefan/7916127/working/building/REAL250005044974 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/88 `/scratch/stefan/7916127/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044974.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044974 none CON=CC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.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, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 103, 103, 103, 46, 28, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 103, 46, 46, 28, 28, 7, 1] 129 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]) total number of confs: 433 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044974 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044974 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044974/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044974 Building REAL250005044975 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044975' /scratch/stefan/7916127/working/building/REAL250005044975 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044975 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044975/0 /scratch/stefan/7916127/working/building/REAL250005044975 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/89 `/scratch/stefan/7916127/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044975.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044975 none C#CCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 153, 78, 155, 155, 78, 78, 27, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 155, 155, 155, 155, 155, 155, 78, 27, 27, 18, 18, 4, 1] 201 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: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044975 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044975 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044975/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044975 Building REAL250005044976 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044976' /scratch/stefan/7916127/working/building/REAL250005044976 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044976 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044976/0 /scratch/stefan/7916127/working/building/REAL250005044976 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/90 `/scratch/stefan/7916127/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(N)=O) `REAL250005044976.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044976 none CN(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(N)=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 153, 77, 77, 77, 36, 25, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 183, 201, 201, 183, 183, 183, 153, 153, 77, 36, 36, 25, 25, 9, 1, 201, 201] 201 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]) total number of confs: 785 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044976 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044976 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044976/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044976 Building REAL250005044977 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044977' /scratch/stefan/7916127/working/building/REAL250005044977 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044977 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044977/0 /scratch/stefan/7916127/working/building/REAL250005044977 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/91 `/scratch/stefan/7916127/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC(=O)N[N-]1)C1=CC(=O)[N-]O1) `REAL250005044977.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044977 none O=C(NCCNC(=O)C1=NC(=O)N[N-]1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 11, 8, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 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: [4, 1, 4, 4, 18, 24, 48, 48, 48, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 4, 18, 18, 24, 24, 48, 78, 1] 78 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005044977 none O=C(NCCNC(=O)C1=NC(=O)N[N-]1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 11, 8, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 76, 49, 41, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 76, 78, 78, 78, 78, 78, 78, 49, 49, 41, 41, 13, 1, 78] 78 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]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044977 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044977 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044977/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044977 Building REAL250005044978 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044978' /scratch/stefan/7916127/working/building/REAL250005044978 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044978 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044978/0 /scratch/stefan/7916127/working/building/REAL250005044978 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/92 `/scratch/stefan/7916127/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(F)CC1)C1=CC(=O)[N-]O1) `REAL250005044978.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044978 none O=C(NCCNC(=O)C1(F)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 34, 43, 111, 111, 111, 184, 184, 184, 1, 1, 1, 1, 1, 1, 9, 34, 34, 43, 43, 111, 184, 184, 184, 184, 1] 184 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044978 none O=C(NCCNC(=O)C1(F)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 105, 71, 12, 12, 1, 12, 1, 1, 1, 1, 174, 184, 184, 184, 184, 184, 174, 105, 105, 71, 71, 12, 1, 1, 1, 1, 184] 184 rigid atoms, others: [6, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044978 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044978 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044978/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044978 Building REAL250005044979 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044979' /scratch/stefan/7916127/working/building/REAL250005044979 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044979 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044979/0 /scratch/stefan/7916127/working/building/REAL250005044979 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/93 `/scratch/stefan/7916127/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C(F)(F)C1CC1)C1=CC(=O)[N-]O1) `REAL250005044979.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044979 none O=C(NCCNC(=O)C(F)(F)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 15, 17, 65, 65, 65, 147, 147, 147, 201, 201, 1, 1, 1, 1, 1, 1, 4, 15, 15, 17, 17, 65, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044979 none O=C(NCCNC(=O)C(F)(F)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 147, 56, 56, 9, 56, 1, 9, 9, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 166, 166, 147, 147, 56, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [8, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044979 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044979 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044979/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044979 Building REAL250005044980 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044980' /scratch/stefan/7916127/working/building/REAL250005044980 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044980 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044980/0 /scratch/stefan/7916127/working/building/REAL250005044980 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/94 `/scratch/stefan/7916127/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCCO)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044980.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044980 none O=C(COCCO)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 108, 164, 188, 201, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 108, 108, 188, 188, 201, 201, 603, 57, 19, 19, 12, 12, 4, 1] 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]) total number of confs: 1335 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044980 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044980 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044980/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044980 Building REAL250005044981 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044981' /scratch/stefan/7916127/working/building/REAL250005044981 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044981 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044981/0 /scratch/stefan/7916127/working/building/REAL250005044981 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/95 `/scratch/stefan/7916127/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005044981.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044981 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 170, 170, 170, 133, 133, 133, 62, 42, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 170, 170, 170, 170, 133, 62, 62, 42, 42, 11, 1] 170 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]) total number of confs: 520 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044981 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 62, 98, 160, 160, 160, 170, 170, 170, 170, 170, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 12, 62, 62, 98, 98, 160, 170] 170 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 637 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044981 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044981 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044981/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044981 Building REAL250005044982 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044982' /scratch/stefan/7916127/working/building/REAL250005044982 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044982 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044982/0 /scratch/stefan/7916127/working/building/REAL250005044982 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/96 `/scratch/stefan/7916127/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC=C(F)C=N1)C1=CC(=O)[N-]O1) `REAL250005044982.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044982 none O=C(NCCNC(=O)C1=NC=C(F)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 24, 36, 75, 75, 75, 85, 85, 77, 85, 85, 85, 1, 1, 1, 1, 1, 1, 7, 24, 24, 36, 36, 75, 85, 85, 1] 85 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 325 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044982 none O=C(NCCNC(=O)C1=NC=C(F)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [43, 43, 32, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 43, 47, 47, 47, 47, 47, 43, 32, 32, 27, 27, 9, 1, 1, 47] 47 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044982 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044982 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044982/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044982 Building REAL250005044983 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044983' /scratch/stefan/7916127/working/building/REAL250005044983 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044983 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044983/0 /scratch/stefan/7916127/working/building/REAL250005044983 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/97 `/scratch/stefan/7916127/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CF)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044983.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044983 none CC(C)(CF)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [178, 90, 178, 179, 201, 90, 90, 28, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 179, 179, 178, 179, 178, 179, 201, 201, 90, 28, 28, 20, 20, 4, 1] 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]) total number of confs: 837 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044983 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044983 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044983/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044983 Building REAL250005044984 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044984' /scratch/stefan/7916127/working/building/REAL250005044984 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044984 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044984/0 /scratch/stefan/7916127/working/building/REAL250005044984 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/98 `/scratch/stefan/7916127/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044984.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044984 none CC(C)[C@@H](O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 201, 131, 164, 164, 65, 65, 65, 26, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 492, 131, 131, 65, 26, 26, 17, 17, 4, 1] 603 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: 1410 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044984 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044984 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044984/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044984 Building REAL250005044985 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044985' /scratch/stefan/7916127/working/building/REAL250005044985 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044985 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044985/0 /scratch/stefan/7916127/working/building/REAL250005044985 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/99 `/scratch/stefan/7916127/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005044985.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044985 none CSC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 92, 92, 92, 31, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 168, 168, 201, 201, 201, 92, 31, 31, 20, 20, 5, 1, 168, 168, 168, 168] 201 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: 597 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044985 none CSC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 10, 10, 10, 53, 81, 164, 165, 164, 168, 168, 168, 168, 168, 1, 1, 6, 6, 6, 10, 53, 53, 81, 81, 165, 168, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 17, 18, 29, 30, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044985 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044985 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044985/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044985 Building REAL250005044986 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044986' /scratch/stefan/7916127/working/building/REAL250005044986 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044986 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044986/0 /scratch/stefan/7916127/working/building/REAL250005044986 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/100 `/scratch/stefan/7916127/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NOCC1)C1=CC(=O)[N-]O1) `REAL250005044986.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044986 none O=C(NCCNC(=O)C1=NOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 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: [10, 1, 10, 10, 30, 36, 87, 87, 87, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 10, 30, 30, 36, 36, 87, 113, 113, 113, 113, 1] 113 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044986 none O=C(NCCNC(=O)C1=NOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 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: [107, 107, 70, 62, 13, 13, 1, 13, 1, 1, 1, 1, 1, 107, 113, 113, 113, 113, 113, 107, 70, 70, 62, 62, 13, 1, 1, 1, 1, 113] 113 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29]) total number of confs: 396 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044986 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044986 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044986/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044986 Building REAL250005044987 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044987' /scratch/stefan/7916127/working/building/REAL250005044987 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044987 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044987/0 /scratch/stefan/7916127/working/building/REAL250005044987 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/101 `/scratch/stefan/7916127/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CCO)CC1)C1=CC(=O)[N-]O1) `REAL250005044987.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044987 none O=C(NCCNC(=O)C1(CCO)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 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: [7, 1, 7, 6, 24, 33, 84, 84, 84, 155, 199, 201, 155, 155, 1, 1, 1, 1, 1, 1, 7, 24, 24, 33, 33, 84, 199, 199, 201, 201, 603, 155, 155, 155, 155, 1] 603 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1355 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044987 none O=C(NCCNC(=O)C1(CCO)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 7, 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: [142, 142, 57, 42, 7, 7, 1, 7, 1, 1, 7, 15, 1, 1, 142, 155, 155, 155, 155, 155, 142, 57, 57, 42, 42, 7, 7, 7, 15, 15, 45, 1, 1, 1, 1, 155] 603 rigid atoms, others: [32, 33, 34, 6, 8, 9, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 587 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044987 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044987 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044987/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044987 Building REAL250005044988 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044988' /scratch/stefan/7916127/working/building/REAL250005044988 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044988 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044988/0 /scratch/stefan/7916127/working/building/REAL250005044988 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/102 `/scratch/stefan/7916127/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044988.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044988 none CC(C)C(C)(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 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, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [193, 184, 201, 120, 184, 182, 120, 120, 44, 27, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 184, 184, 184, 552, 120, 44, 44, 27, 27, 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: 1410 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044988 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044988 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044988/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044988 Building REAL250005044989 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044989' /scratch/stefan/7916127/working/building/REAL250005044989 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044989 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044989/0 /scratch/stefan/7916127/working/building/REAL250005044989 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/103 `/scratch/stefan/7916127/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005044989.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044989 none CC1(C)CC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 109, 127, 109, 109, 53, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 109, 53, 53, 36, 36, 11, 1, 127, 127] 127 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: 440 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: REAL250005044989 none CC1(C)CC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 18, 34, 115, 115, 115, 127, 127, 127, 127, 127, 1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 3, 18, 18, 34, 34, 115, 127, 1, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 20, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 405 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044989 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044989 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044989/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044989 Building REAL250005044990 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044990' /scratch/stefan/7916127/working/building/REAL250005044990 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044990 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044990/0 /scratch/stefan/7916127/working/building/REAL250005044990 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/104 `/scratch/stefan/7916127/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCSC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044990.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044990 none CC1CCSC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 69, 69, 69, 35, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 69, 35, 35, 24, 24, 9, 1] 77 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: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044990 none CC1CCSC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 14, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 1, 3, 3, 3, 16, 30, 72, 72, 72, 77, 77, 77, 77, 77, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 16, 16, 30, 30, 72, 77] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 269 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044990 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044990 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044990/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044990 Building REAL250005044991 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044991' /scratch/stefan/7916127/working/building/REAL250005044991 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044991 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044991/0 /scratch/stefan/7916127/working/building/REAL250005044991 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/105 `/scratch/stefan/7916127/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C[NH+](C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044991.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044991 none CC(C[NH+](C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1] 8 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: 34 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044991 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044991 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044991/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044991 Building REAL250005044992 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044992' /scratch/stefan/7916127/working/building/REAL250005044992 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044992 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044992/0 /scratch/stefan/7916127/working/building/REAL250005044992 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/106 `/scratch/stefan/7916127/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1) `REAL250005044992.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044992 none CN1C=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 183, 82, 82, 82, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 183, 183, 82, 33, 33, 20, 20, 4, 1] 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]) total number of confs: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044992 none CN1C=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 35, 35, 35, 79, 114, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 8, 8, 35, 79, 79, 114, 114, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044992 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044992 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044992/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044992 Building REAL250005044993 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044993' /scratch/stefan/7916127/working/building/REAL250005044993 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044993 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044993/0 /scratch/stefan/7916127/working/building/REAL250005044993 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/107 `/scratch/stefan/7916127/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NN=CS1)C1=CC(=O)[N-]O1) `REAL250005044993.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044993 none O=C(NCCNC(=O)C1=NN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 28, 33, 67, 67, 67, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 9, 28, 28, 33, 33, 67, 89, 1] 89 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044993 none O=C(NCCNC(=O)C1=NN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [87, 87, 53, 37, 9, 9, 1, 9, 1, 1, 1, 1, 1, 87, 89, 89, 89, 89, 89, 87, 53, 53, 37, 37, 9, 1, 89] 89 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044993 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044993 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044993/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044993 Building REAL250005044994 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044994' /scratch/stefan/7916127/working/building/REAL250005044994 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044994 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044994/0 /scratch/stefan/7916127/working/building/REAL250005044994 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/108 `/scratch/stefan/7916127/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1[C@H]2CCCO[C@H]21)C1=CC(=O)[N-]O1) `REAL250005044994.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044994 none O=C(NCCNC(=O)[C@@H]1[C@H]2CCCO[C@H]21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 44, 112, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 28, 28, 44, 44, 112, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 36, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 650 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: REAL250005044994 none O=C(NCCNC(=O)[C@@H]1[C@H]2CCCO[C@H]21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 12, 5, 7, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 108, 70, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 195, 108, 108, 70, 70, 13, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 731 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044994 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044994 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044994/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044994 Building REAL250005044995 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044995' /scratch/stefan/7916127/working/building/REAL250005044995 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044995 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044995/0 /scratch/stefan/7916127/working/building/REAL250005044995 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/109 `/scratch/stefan/7916127/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SN=C1) `REAL250005044995.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044995 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SN=C1 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', 'S.3', 'N.2', 'C.2', '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, 14, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 125, 125, 125, 54, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 125, 54, 54, 30, 30, 9, 1, 201] 201 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]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044995 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SN=C1 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', 'S.3', 'N.2', 'C.2', '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, 14, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 53, 95, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 53, 53, 95, 95, 193, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044995 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044995 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044995/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044995 Building REAL250005044996 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044996' /scratch/stefan/7916127/working/building/REAL250005044996 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044996 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044996/0 /scratch/stefan/7916127/working/building/REAL250005044996 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/110 `/scratch/stefan/7916127/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C(F)C1CCC1)C1=CC(=O)[N-]O1) `REAL250005044996.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044996 none O=C(NCCNC(=O)C(F)C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 17, 26, 79, 79, 79, 160, 160, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 17, 17, 26, 26, 79, 160, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 803 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044996 none O=C(NCCNC(=O)C(F)C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 143, 123, 36, 36, 6, 36, 1, 6, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 143, 143, 123, 123, 36, 6, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 8, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044996 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044996 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044996/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044996 Building REAL250005044997 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044997' /scratch/stefan/7916127/working/building/REAL250005044997 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044997 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044997/0 /scratch/stefan/7916127/working/building/REAL250005044997 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/111 `/scratch/stefan/7916127/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC(F)F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005044997.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044997 none CC(OC(F)F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 15, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 77, 145, 185, 201, 201, 77, 77, 26, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 146, 145, 146, 146, 201, 77, 26, 26, 15, 15, 4, 1] 201 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]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044997 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044997 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044997/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044997 Building REAL250005044998 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044998' /scratch/stefan/7916127/working/building/REAL250005044998 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044998 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044998/0 /scratch/stefan/7916127/working/building/REAL250005044998 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/112 `/scratch/stefan/7916127/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005044998.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044998 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 114, 90, 90, 91, 48, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 91, 48, 48, 31, 31, 7, 1] 114 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]) total number of confs: 393 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044998 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 71, 111, 111, 111, 114, 114, 114, 114, 114, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 43, 43, 71, 71, 111, 114] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044998 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044998 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044998/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044998 Building REAL250005044999 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005044999' /scratch/stefan/7916127/working/building/REAL250005044999 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005044999 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005044999/0 /scratch/stefan/7916127/working/building/REAL250005044999 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/113 `/scratch/stefan/7916127/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005044999.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005044999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005044999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005044999 none C#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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, 90, 90, 90, 90, 79, 79, 79, 34, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 79, 34, 34, 22, 22, 7, 1] 90 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]) 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: REAL250005044999 none C#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 29, 46, 85, 85, 85, 90, 90, 90, 90, 90, 1, 1, 1, 1, 7, 29, 29, 46, 46, 85, 90] 90 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005044999 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005044999 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005044999/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005044999 Building REAL250005045000 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045000' /scratch/stefan/7916127/working/building/REAL250005045000 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045000 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045000/0 /scratch/stefan/7916127/working/building/REAL250005045000 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/114 `/scratch/stefan/7916127/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005045000.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045000 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 125, 125, 126, 63, 40, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 126, 63, 63, 40, 40, 9, 1] 156 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]) total number of confs: 497 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045000 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 57, 93, 139, 140, 139, 156, 156, 156, 156, 156, 1, 1, 2, 2, 2, 1, 1, 1, 13, 57, 57, 93, 93, 140, 156] 156 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045000 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045000 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045000/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045000 Building REAL250005045001 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045001' /scratch/stefan/7916127/working/building/REAL250005045001 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045001 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045001/0 /scratch/stefan/7916127/working/building/REAL250005045001 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/115 `/scratch/stefan/7916127/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N=[N+]=[N-]) `REAL250005045001.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045001 none CC(C)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N=[N+]=[N-] NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'N.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 65, 124, 34, 34, 34, 18, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 125, 201, 201, 125, 125, 125, 125, 125, 125, 65, 65, 34, 18, 18, 11, 11, 3, 1] 201 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]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045001 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045001 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045001/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045001 Building REAL250005045002 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045002' /scratch/stefan/7916127/working/building/REAL250005045002 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045002 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045002/0 /scratch/stefan/7916127/working/building/REAL250005045002 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/116 `/scratch/stefan/7916127/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(F)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045002.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045002 none CC1(F)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 114, 114, 114, 50, 32, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 50, 50, 32, 32, 9, 1, 201, 201] 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]) total number of confs: 663 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: REAL250005045002 none CC1(F)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 13, 13, 13, 63, 104, 188, 189, 188, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 13, 63, 63, 104, 104, 189, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 19, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 742 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045002 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045002 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045002/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045002 Building REAL250005045003 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045003' /scratch/stefan/7916127/working/building/REAL250005045003 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045003 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045003/0 /scratch/stefan/7916127/working/building/REAL250005045003 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/117 `/scratch/stefan/7916127/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(=O)NC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045003.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045003 none O=C(CC(=O)NC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 116, 153, 153, 153, 201, 201, 21, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 116, 116, 153, 201, 201, 201, 201, 201, 52, 21, 21, 16, 16, 4, 1] 201 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: 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: REAL250005045003 none O=C(CC(=O)NC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 1, 11, 8, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 6, 4, 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] 0 hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 89, 89, 188, 191, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 6, 1, 1, 1, 1, 1, 90, 188, 188, 191, 191, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 787 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045003 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045003 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045003/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045003 Building REAL250005045004 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045004' /scratch/stefan/7916127/working/building/REAL250005045004 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045004 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045004/0 /scratch/stefan/7916127/working/building/REAL250005045004 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/118 `/scratch/stefan/7916127/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045004.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045004 none COCC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 158, 95, 158, 95, 95, 32, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 158, 474, 95, 32, 32, 22, 22, 4, 1] 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]) total number of confs: 1329 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045004 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045004 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045004/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045004 Building REAL250005045005 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045005' /scratch/stefan/7916127/working/building/REAL250005045005 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045005 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045005/0 /scratch/stefan/7916127/working/building/REAL250005045005 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/119 `/scratch/stefan/7916127/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1) `REAL250005045005.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045005 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 14, 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, 7, 6, 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] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 171, 108, 108, 108, 38, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 171, 171, 171, 171, 171, 171, 171, 171, 171, 171, 108, 38, 38, 26, 26, 9, 1] 171 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]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045005 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 14, 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, 7, 6, 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] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 66, 102, 164, 165, 165, 171, 171, 171, 171, 171, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 66, 66, 102, 102, 165, 171] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045005 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045005 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045005/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045005 Building REAL250005045006 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045006' /scratch/stefan/7916127/working/building/REAL250005045006 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045006 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045006/0 /scratch/stefan/7916127/working/building/REAL250005045006 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/120 `/scratch/stefan/7916127/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045006.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045006 none C#CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 105, 201, 201, 105, 105, 51, 29, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 105, 51, 51, 29, 29, 7, 1] 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]) total number of confs: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045006 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045006 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045006/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045006 Building REAL250005045007 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045007' /scratch/stefan/7916127/working/building/REAL250005045007 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045007 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045007/0 /scratch/stefan/7916127/working/building/REAL250005045007 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/121 `/scratch/stefan/7916127/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045007.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045007 none O=C(C=CC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 177, 177, 201, 201, 201, 201, 36, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 201, 83, 36, 36, 26, 26, 6, 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: 633 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045007 none O=C(C=CC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 8, 1, 1, 1, 1, 1, 1, 39, 39, 101, 134, 199, 199, 199, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 39, 101, 101, 134, 134, 199, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045007 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045007 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045007/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045007 Building REAL250005045008 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045008' /scratch/stefan/7916127/working/building/REAL250005045008 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045008 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045008/0 /scratch/stefan/7916127/working/building/REAL250005045008 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/122 `/scratch/stefan/7916127/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045008.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045008 none COC(C)C(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 157, 201, 105, 158, 105, 105, 35, 23, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 158, 474, 105, 35, 35, 23, 23, 4, 1] 603 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: 1328 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045008 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045008 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045008/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045008 Building REAL250005045009 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045009' /scratch/stefan/7916127/working/building/REAL250005045009 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045009 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045009/0 /scratch/stefan/7916127/working/building/REAL250005045009 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/123 `/scratch/stefan/7916127/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1CNC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045009.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045009 none O=C(NCCNC(=O)[C@H]1CNC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 29, 40, 98, 98, 98, 152, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 1, 9, 29, 29, 40, 40, 98, 152, 152, 152, 152, 1] 152 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 506 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: REAL250005045009 none O=C(NCCNC(=O)[C@H]1CNC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 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: [143, 143, 87, 63, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 143, 152, 152, 152, 152, 152, 143, 87, 87, 63, 63, 12, 1, 1, 1, 1, 152] 152 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 558 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045009 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045009 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045009/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045009 Building REAL250005045010 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045010' /scratch/stefan/7916127/working/building/REAL250005045010 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045010 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045010/0 /scratch/stefan/7916127/working/building/REAL250005045010 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/124 `/scratch/stefan/7916127/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045010.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045010 none CCSC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 131, 78, 131, 78, 78, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 131, 131, 131, 131, 78, 25, 25, 16, 16, 4, 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: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045010 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045010 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045010/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045010 Building REAL250005045011 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045011' /scratch/stefan/7916127/working/building/REAL250005045011 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045011 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045011/0 /scratch/stefan/7916127/working/building/REAL250005045011 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/125 `/scratch/stefan/7916127/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+]1CC(C)C1) `REAL250005045011.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045011 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+]1CC(C)C1 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', 'N.4', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 11, 11, 11, 17, 21, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 17, 17, 21, 21, 28, 28, 1, 1, 1, 2, 2, 2, 1, 1] 28 rigid atoms, others: [1, 34, 35, 33, 40, 39, 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, 36, 37, 38]) 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: REAL250005045011 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+]1CC(C)C1 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', 'N.4', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 25, 16, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 25, 16, 16, 14, 14, 6, 1, 28, 28, 28, 28, 28, 28, 28, 28] 28 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, 36, 37, 38, 39, 40]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045011 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045011/1 /scratch/stefan/7916127/working/building/REAL250005045011 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/126 `/scratch/stefan/7916127/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1CC(C)C1) `REAL250005045011.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045011 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1CC(C)C1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 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: [3, 1, 3, 14, 14, 14, 54, 84, 160, 160, 160, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 3, 3, 3, 3, 14, 54, 54, 84, 84, 160, 161, 1, 1, 1, 2, 2, 2, 1, 1] 161 rigid atoms, others: [32, 1, 34, 38, 33, 39, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37]) total number of confs: 591 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045011 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1CC(C)C1 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', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 114, 114, 114, 39, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 161, 161, 114, 39, 39, 23, 23, 5, 1, 161, 161, 161, 161, 161, 161, 161, 161] 161 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 580 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045011 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045011 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045011/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045011/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045011 Building REAL250005045012 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045012' /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045012 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045012/0 /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/127 `/scratch/stefan/7916127/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045012.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045012 none CC1CCN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.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', '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, 10, 5, 1, 11, 8, 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, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 194, 125, 125, 125, 44, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 194, 194, 125, 44, 44, 26, 26, 5, 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: 786 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045012 none CC1CCN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.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', '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, 10, 5, 1, 11, 8, 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, 7, 7, 6, 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] 0 hydrogens 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, 22, 22, 22, 86, 124, 200, 201, 200, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 22, 86, 86, 124, 123, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 23, 24, 25, 26, 27] set([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: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045012/1 /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/128 `/scratch/stefan/7916127/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045012.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045012 none CC1CC[N@@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 23, 23, 23, 17, 14, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 17, 17, 14, 14, 3, 1] 26 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: 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: REAL250005045012 none CC1CC[N@@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 19, 20, 26, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 15, 19, 19, 20, 20, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045012/2 /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/129 `/scratch/stefan/7916127/working/3D/129' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045012.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045012/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045012 none CC1CC[N@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 1, 7, 7, 7, 6, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 21, 22, 20, 20, 20, 13, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 21, 21, 20, 13, 13, 12, 12, 4, 1] 22 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: 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: REAL250005045012 none CC1CC[N@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 1, 7, 7, 7, 6, 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] 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, 1, 6, 13, 13, 13, 17, 20, 22, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 13, 17, 17, 20, 20, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045012 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045012 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045012/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045012/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045012/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045012 Building REAL250005045013 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045013' /scratch/stefan/7916127/working/building/REAL250005045013 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045013 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045013/0 /scratch/stefan/7916127/working/building/REAL250005045013 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/130 `/scratch/stefan/7916127/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045013.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045013 none COC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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, 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: [19, 10, 1, 10, 10, 22, 22, 22, 67, 85, 121, 122, 121, 122, 122, 122, 122, 122, 1, 1, 1, 19, 19, 19, 10, 10, 10, 22, 67, 67, 85, 85, 122, 122, 1, 1, 1, 1, 1] 122 rigid atoms, others: [34, 35, 36, 37, 38, 2, 18, 19, 20] set([0, 1, 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, 32, 33]) 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: REAL250005045013 none COC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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, 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: [115, 107, 69, 107, 69, 69, 28, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 107, 122, 122, 115, 115, 115, 107, 107, 107, 69, 28, 28, 16, 16, 4, 1, 122, 122, 122, 122, 122] 122 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: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045013 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045013 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045013/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045013 Building REAL250005045014 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045014' /scratch/stefan/7916127/working/building/REAL250005045014 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045014 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045014/0 /scratch/stefan/7916127/working/building/REAL250005045014 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/131 `/scratch/stefan/7916127/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045014.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045014 none O=C(COC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 134, 169, 201, 201, 22, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 134, 134, 201, 201, 201, 201, 201, 71, 22, 22, 13, 13, 4, 1] 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]) total number of confs: 715 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045014 none O=C(COC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 21, 6, 1, 1, 1, 1, 51, 51, 127, 142, 201, 201, 201, 201, 201, 201, 201, 201, 21, 21, 1, 1, 1, 1, 1, 51, 127, 127, 142, 142, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 21, 22, 23, 24, 25] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045014 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045014 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045014/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045014 Building REAL250005045015 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045015' /scratch/stefan/7916127/working/building/REAL250005045015 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045015 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045015/0 /scratch/stefan/7916127/working/building/REAL250005045015 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/132 `/scratch/stefan/7916127/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC=CN1)C1=CC(=O)[N-]O1) `REAL250005045015.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045015 none O=C(NCCNC(=O)C1=NC=CN1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 25, 35, 58, 58, 58, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 8, 25, 25, 35, 35, 58, 59, 59, 59, 1] 59 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045015 none O=C(NCCNC(=O)C1=NC=CN1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 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, 26, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 26, 26, 18, 18, 7, 1, 1, 1, 37] 37 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045015 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045015 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045015/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045015 Building REAL250005045016 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045016' /scratch/stefan/7916127/working/building/REAL250005045016 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045016 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045016/0 /scratch/stefan/7916127/working/building/REAL250005045016 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/133 `/scratch/stefan/7916127/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045016.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045016 none O=C(C=CC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 171, 171, 201, 201, 201, 37, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 201, 89, 37, 37, 24, 24, 6, 1] 201 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: 664 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: REAL250005045016 none O=C(C=CC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens 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, 7, 7, 1, 1, 1, 1, 1, 33, 33, 103, 135, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 33, 103, 103, 135, 135, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 768 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045016 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045016 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045016/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045016 Building REAL250005045017 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045017' /scratch/stefan/7916127/working/building/REAL250005045017 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045017 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045017/0 /scratch/stefan/7916127/working/building/REAL250005045017 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/134 `/scratch/stefan/7916127/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005045017.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045017 none COC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 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, 200, 136, 136, 137, 52, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 200, 200, 137, 52, 52, 32, 32, 7, 1, 200, 200, 200, 200, 200, 200, 200, 200] 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, 35, 36, 37, 38]) total number of confs: 655 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: REAL250005045017 none COC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 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: [6, 1, 1, 1, 9, 9, 9, 49, 85, 196, 198, 196, 201, 201, 201, 201, 200, 1, 1, 1, 1, 6, 6, 6, 9, 49, 49, 85, 85, 198, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 34, 17, 18, 19, 20, 38, 31] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 708 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045017 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045017 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045017/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045017 Building REAL250005045018 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045018' /scratch/stefan/7916127/working/building/REAL250005045018 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045018 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045018/0 /scratch/stefan/7916127/working/building/REAL250005045018 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/135 `/scratch/stefan/7916127/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1NC(=O)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045018.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045018 none CN1NC(=O)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 194, 194, 194, 194, 134, 134, 134, 51, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 134, 51, 51, 32, 32, 9, 1] 194 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: 531 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: REAL250005045018 none CN1NC(=O)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 105, 188, 190, 188, 194, 194, 194, 194, 194, 2, 2, 2, 1, 1, 12, 65, 65, 105, 105, 190, 194] 194 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 731 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045018 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045018 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045018/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045018 Building REAL250005045019 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045019' /scratch/stefan/7916127/working/building/REAL250005045019 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045019 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045019/0 /scratch/stefan/7916127/working/building/REAL250005045019 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/136 `/scratch/stefan/7916127/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045019.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045019 none CCC1=CNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 137, 137, 137, 137, 99, 99, 99, 34, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 137, 137, 99, 34, 34, 22, 22, 5, 1, 137] 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]) 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: REAL250005045019 none CCC1=CNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 10, 10, 10, 39, 57, 129, 129, 129, 137, 137, 137, 137, 137, 1, 9, 9, 9, 8, 8, 1, 1, 10, 38, 38, 57, 57, 129, 137, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045019 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045019 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045019/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045019 Building REAL250005045020 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045020' /scratch/stefan/7916127/working/building/REAL250005045020 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045020 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045020/0 /scratch/stefan/7916127/working/building/REAL250005045020 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/137 `/scratch/stefan/7916127/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045020.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045020 none CCCC=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 150, 113, 113, 58, 58, 58, 23, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 150, 150, 113, 113, 58, 23, 23, 15, 15, 4, 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: 846 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045020 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045020 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045020/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045020 Building REAL250005045021 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045021' /scratch/stefan/7916127/working/building/REAL250005045021 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045021 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045021/0 /scratch/stefan/7916127/working/building/REAL250005045021 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/138 `/scratch/stefan/7916127/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045021.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045021 none CC=C(F)C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.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, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 89, 107, 89, 89, 47, 29, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 89, 47, 47, 29, 29, 9, 1] 107 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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045021 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045021 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045021/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045021 Building REAL250005045022 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045022' /scratch/stefan/7916127/working/building/REAL250005045022 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045022 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045022/0 /scratch/stefan/7916127/working/building/REAL250005045022 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/139 `/scratch/stefan/7916127/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NSNC1=O)C1=CC(=O)[N-]O1) `REAL250005045022.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045022 none O=C(NCCNC(=O)C1=NSNC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 28, 35, 77, 77, 77, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 11, 28, 28, 35, 35, 77, 147, 1] 147 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045022 none O=C(NCCNC(=O)C1=NSNC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 14, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 89, 69, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 141, 147, 147, 147, 147, 147, 141, 89, 89, 69, 69, 13, 1, 147] 147 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]) total number of confs: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045022 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045022 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045022/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045022 Building REAL250005045023 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045023' /scratch/stefan/7916127/working/building/REAL250005045023 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045023 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045023/0 /scratch/stefan/7916127/working/building/REAL250005045023 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/140 `/scratch/stefan/7916127/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005045023.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045023 none CCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C 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', 'H', '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, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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: [177, 174, 94, 94, 94, 39, 26, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 174, 197, 197, 187, 187, 187, 187, 187, 174, 94, 39, 39, 26, 26, 5, 1, 197, 197, 197, 197, 197, 197, 197] 201 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]) total number of confs: 975 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045023 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045023 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045023/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045023 Building REAL250005045024 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045024' /scratch/stefan/7916127/working/building/REAL250005045024 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045024 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045024/0 /scratch/stefan/7916127/working/building/REAL250005045024 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/141 `/scratch/stefan/7916127/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045024.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045024 none CSC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 98, 164, 164, 98, 98, 36, 24, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 165, 164, 165, 165, 165, 164, 98, 36, 36, 24, 24, 4, 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: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045024 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045024 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045024/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045024 Building REAL250005045025 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045025' /scratch/stefan/7916127/working/building/REAL250005045025 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045025 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045025/0 /scratch/stefan/7916127/working/building/REAL250005045025 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/142 `/scratch/stefan/7916127/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=NS1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045025.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045025 none O=C(CC1=CN=NS1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 8, 14, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 134, 201, 201, 201, 201, 25, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 134, 134, 201, 59, 25, 25, 18, 18, 4, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 615 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045025 none O=C(CC1=CN=NS1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 8, 14, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 32, 33, 124, 152, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 1, 32, 124, 124, 152, 152, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045025 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045025 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045025/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045025 Building REAL250005045026 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045026' /scratch/stefan/7916127/working/building/REAL250005045026 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045026 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045026/0 /scratch/stefan/7916127/working/building/REAL250005045026 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/143 `/scratch/stefan/7916127/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=C1CCC1) `REAL250005045026.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045026 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [9, 1, 9, 9, 49, 81, 149, 149, 149, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 9, 49, 49, 81, 81, 149, 159, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 574 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045026 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=C1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [125, 125, 57, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 125, 159, 159, 159, 159, 159, 125, 57, 57, 36, 36, 11, 1, 159, 159, 159, 159, 159, 159] 159 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: 528 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045026 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045026 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045026/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045026 Building REAL250005045027 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045027' /scratch/stefan/7916127/working/building/REAL250005045027 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045027 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045027/0 /scratch/stefan/7916127/working/building/REAL250005045027 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/144 `/scratch/stefan/7916127/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045027.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045027 none CCC(CO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [165, 151, 81, 151, 190, 81, 81, 33, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 151, 190, 190, 570, 81, 33, 33, 20, 20, 4, 1] 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]) total number of confs: 1604 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045027 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045027 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045027/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045027 Building REAL250005045028 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045028' /scratch/stefan/7916127/working/building/REAL250005045028 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045028 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045028/0 /scratch/stefan/7916127/working/building/REAL250005045028 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/145 `/scratch/stefan/7916127/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045028.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045028 none CC(C)(O)C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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 330 conformations in input total number of sets (complete confs): 330 using faster count positions algorithm for large data unique positions, atoms: [110, 88, 109, 110, 68, 88, 68, 68, 33, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 110, 330, 88, 68, 33, 33, 22, 22, 6, 1] 330 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: 787 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045028 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045028 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045028/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045028 Building REAL250005045029 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045029' /scratch/stefan/7916127/working/building/REAL250005045029 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045029 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045029/0 /scratch/stefan/7916127/working/building/REAL250005045029 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/146 `/scratch/stefan/7916127/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045029.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045029 none CC(C)CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 12, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 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, 152, 126, 45, 45, 45, 18, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 126, 126, 45, 18, 18, 11, 11, 3, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045029 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045029 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045029/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045029 Building REAL250005045030 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045030' /scratch/stefan/7916127/working/building/REAL250005045030 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045030 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045030/0 /scratch/stefan/7916127/working/building/REAL250005045030 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/147 `/scratch/stefan/7916127/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045030.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045030 none CC(CO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [183, 90, 183, 201, 90, 90, 32, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 184, 184, 183, 184, 201, 201, 603, 90, 32, 32, 20, 20, 4, 1] 603 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]) total number of confs: 1425 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045030 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045030 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045030/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045030 Building REAL250005045031 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045031' /scratch/stefan/7916127/working/building/REAL250005045031 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045031 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045031/0 /scratch/stefan/7916127/working/building/REAL250005045031 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/148 `/scratch/stefan/7916127/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CON=C1) `REAL250005045031.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045031 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [5, 1, 5, 5, 33, 72, 134, 134, 134, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 5, 33, 33, 72, 72, 134, 142, 1, 1] 142 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 524 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045031 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CON=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [92, 92, 40, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 92, 142, 142, 142, 142, 92, 40, 40, 30, 30, 8, 1, 142, 142] 142 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045031 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045031 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045031/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045031 Building REAL250005045032 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045032' /scratch/stefan/7916127/working/building/REAL250005045032 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045032 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045032/0 /scratch/stefan/7916127/working/building/REAL250005045032 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/149 `/scratch/stefan/7916127/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045032.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045032 none O=C(C=CC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [101, 101, 101, 159, 159, 183, 183, 183, 183, 45, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 159, 159, 183, 183, 183, 101, 45, 45, 28, 28, 9, 1] 183 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: 565 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045032 none O=C(C=CC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [37, 8, 8, 1, 1, 1, 1, 1, 1, 38, 38, 104, 133, 169, 169, 169, 183, 183, 183, 183, 183, 8, 8, 1, 1, 1, 38, 104, 104, 133, 133, 169, 183] 183 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045032 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045032 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045032/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045032 Building REAL250005045033 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045033' /scratch/stefan/7916127/working/building/REAL250005045033 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045033 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045033/0 /scratch/stefan/7916127/working/building/REAL250005045033 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/150 `/scratch/stefan/7916127/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1=NC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045033.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045033 none O=C(C=CC1=NC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 161, 161, 162, 162, 162, 162, 44, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 161, 161, 162, 162, 162, 95, 44, 44, 32, 32, 9, 1] 162 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: 533 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045033 none O=C(C=CC1=NC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [22, 6, 6, 1, 1, 1, 1, 1, 1, 22, 22, 53, 67, 104, 104, 104, 110, 110, 110, 110, 110, 6, 6, 1, 1, 1, 22, 53, 53, 67, 67, 104, 110] 110 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 415 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045033 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045033 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045033/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045033 Building REAL250005045034 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045034' /scratch/stefan/7916127/working/building/REAL250005045034 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045034 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045034/0 /scratch/stefan/7916127/working/building/REAL250005045034 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/151 `/scratch/stefan/7916127/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)COC1) `REAL250005045034.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045034 none CCC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)COC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 149, 111, 40, 40, 40, 29, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 149, 149, 149, 151, 151, 151, 151, 151, 111, 111, 40, 29, 29, 20, 20, 4, 1, 149, 149, 149, 149] 151 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]) total number of confs: 596 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: REAL250005045034 none CCC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)COC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 8, 24, 24, 24, 64, 74, 149, 149, 149, 149, 149, 149, 149, 149, 1, 1, 1, 3, 3, 3, 3, 3, 8, 8, 24, 64, 64, 74, 74, 149, 149, 1, 1, 1, 1] 151 rigid atoms, others: [1, 2, 3, 36, 37, 35, 18, 19, 20, 38] set([0, 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, 32, 33, 34]) total number of confs: 524 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045034 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045034 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045034/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045034 Building REAL250005045035 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045035' /scratch/stefan/7916127/working/building/REAL250005045035 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045035 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045035/0 /scratch/stefan/7916127/working/building/REAL250005045035 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/152 `/scratch/stefan/7916127/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1=CNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045035.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045035 none O=C(C=CC1=CNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [125, 125, 125, 192, 192, 192, 192, 192, 192, 54, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 125, 54, 54, 37, 37, 11, 1] 192 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: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045035 none O=C(C=CC1=CNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [35, 6, 6, 1, 1, 1, 1, 1, 1, 35, 35, 95, 116, 164, 165, 164, 174, 174, 174, 174, 174, 6, 6, 1, 1, 1, 35, 95, 95, 116, 116, 165, 174] 174 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 656 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045035 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045035 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045035/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045035 Building REAL250005045036 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045036' /scratch/stefan/7916127/working/building/REAL250005045036 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045036 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045036/0 /scratch/stefan/7916127/working/building/REAL250005045036 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/153 `/scratch/stefan/7916127/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1C[C@H]1CF)C1=CC(=O)[N-]O1) `REAL250005045036.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045036 none O=C(NCCNC(=O)[C@@H]1C[C@H]1CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 16, 25, 75, 75, 75, 191, 191, 191, 191, 191, 201, 1, 1, 1, 1, 1, 1, 3, 15, 15, 25, 25, 75, 191, 191, 201, 201, 1] 201 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045036 none O=C(NCCNC(=O)[C@@H]1C[C@H]1CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 85, 64, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 9, 187, 191, 191, 191, 191, 191, 187, 85, 85, 64, 64, 12, 1, 1, 9, 9, 191] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045036 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045036 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045036/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045036 Building REAL250005045037 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045037' /scratch/stefan/7916127/working/building/REAL250005045037 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045037 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045037/0 /scratch/stefan/7916127/working/building/REAL250005045037 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/154 `/scratch/stefan/7916127/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CCCC[C@H]1O)C1=CC(=O)[N-]O1) `REAL250005045037.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045037 none O=C(NCCNC(=O)[C@@H]1CCCC[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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, 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: [8, 1, 8, 8, 32, 48, 118, 118, 118, 178, 178, 178, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 9, 31, 31, 48, 48, 118, 178, 178, 178, 178, 178, 178, 178, 178, 534, 1] 534 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: 1123 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045037 none O=C(NCCNC(=O)[C@@H]1CCCC[C@H]1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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, 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: [172, 172, 93, 62, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 172, 178, 178, 178, 178, 178, 172, 93, 93, 62, 62, 9, 1, 1, 1, 1, 1, 1, 1, 1, 3, 178] 534 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045037 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045037 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045037/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045037 Building REAL250005045038 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045038' /scratch/stefan/7916127/working/building/REAL250005045038 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045038 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045038/0 /scratch/stefan/7916127/working/building/REAL250005045038 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/155 `/scratch/stefan/7916127/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CCCC1) `REAL250005045038.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045038 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CCCC1 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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 116, 116, 116, 51, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 116, 51, 51, 32, 32, 7, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 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: 674 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045038 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CCCC1 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.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 48, 83, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 7, 48, 48, 83, 83, 193, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 16, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 702 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045038 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045038 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045038/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045038 Building REAL250005045039 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045039' /scratch/stefan/7916127/working/building/REAL250005045039 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045039 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045039/0 /scratch/stefan/7916127/working/building/REAL250005045039 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/156 `/scratch/stefan/7916127/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC2(CC2)C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045039.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045039 none O=C(CC1CC2(CC2)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 149, 201, 201, 201, 201, 201, 29, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 53, 29, 29, 20, 20, 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: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045039 none O=C(CC1CC2(CC2)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 6, 1, 1, 1, 1, 1, 1, 1, 35, 35, 118, 138, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 118, 118, 138, 138, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045039 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045039 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045039/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045039 Building REAL250005045040 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045040' /scratch/stefan/7916127/working/building/REAL250005045040 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045040 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045040/0 /scratch/stefan/7916127/working/building/REAL250005045040 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/157 `/scratch/stefan/7916127/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN1C) `REAL250005045040.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045040 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 79, 79, 79, 43, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 169, 169, 79, 43, 43, 28, 28, 7, 1, 169, 169, 169, 169] 169 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: 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: REAL250005045040 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 29, 68, 152, 152, 152, 169, 169, 169, 169, 169, 1, 1, 1, 2, 2, 2, 1, 5, 29, 29, 68, 68, 152, 169, 1, 2, 2, 2] 169 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35]) total number of confs: 602 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045040 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045040 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045040/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045040 Building REAL250005045041 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045041' /scratch/stefan/7916127/working/building/REAL250005045041 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045041 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045041/0 /scratch/stefan/7916127/working/building/REAL250005045041 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/158 `/scratch/stefan/7916127/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCOC1) `REAL250005045041.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045041 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCOC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 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, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 15, 15, 15, 57, 79, 147, 147, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 57, 57, 79, 79, 147, 147, 1, 1, 1, 1, 1, 1, 1] 147 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 535 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045041 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCOC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 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, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 94, 94, 94, 37, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 147, 147, 147, 94, 37, 37, 22, 22, 4, 1, 147, 147, 147, 147, 147, 147, 147] 147 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045041 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045041 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045041/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045041 Building REAL250005045042 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045042' /scratch/stefan/7916127/working/building/REAL250005045042 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045042 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045042/0 /scratch/stefan/7916127/working/building/REAL250005045042 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/159 `/scratch/stefan/7916127/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(Cl)=C1) `REAL250005045042.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045042 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [5, 1, 5, 5, 31, 65, 132, 132, 132, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 5, 31, 31, 65, 65, 132, 145, 1, 1] 145 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045042 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(Cl)=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'Cl', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 16, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [99, 99, 46, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 99, 145, 145, 145, 145, 145, 99, 46, 46, 32, 32, 11, 1, 145, 145] 145 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]) total number of confs: 420 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045042 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045042 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045042/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045042 Building REAL250005045043 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045043' /scratch/stefan/7916127/working/building/REAL250005045043 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045043 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045043/0 /scratch/stefan/7916127/working/building/REAL250005045043 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/160 `/scratch/stefan/7916127/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)[C@H]1C[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045043.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045043 none C[NH+](C)[C@H]1C[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 30, 30, 30, 30, 24, 30, 24, 24, 18, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 24, 18, 18, 17, 17, 7, 1, 30, 30] 30 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, 39, 40]) 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: REAL250005045043 none C[NH+](C)[C@H]1C[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 18, 22, 22, 22, 30, 30, 30, 30, 30, 1, 2, 2, 2, 2, 2, 2, 1, 1, 8, 16, 16, 18, 18, 22, 30, 1, 1] 30 rigid atoms, others: [1, 4, 5, 6, 7, 8, 9, 39, 40, 23, 30, 31] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045043 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045043 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045043/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045043 Building REAL250005045044 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045044' /scratch/stefan/7916127/working/building/REAL250005045044 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045044 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045044/0 /scratch/stefan/7916127/working/building/REAL250005045044 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/161 `/scratch/stefan/7916127/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC[NH+](C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045044.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045044 none CC(CC[NH+](C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', '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, 9, 6, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 14, 14, 16, 16, 16, 11, 11, 10, 8, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 14, 14, 14, 14, 16, 16, 16, 16, 16, 16, 11, 10, 10, 8, 8, 4, 1] 16 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: 74 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045044 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045044 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045044/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045044 Building REAL250005045045 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045045' /scratch/stefan/7916127/working/building/REAL250005045045 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045045 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045045/0 /scratch/stefan/7916127/working/building/REAL250005045045 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/162 `/scratch/stefan/7916127/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC(C2CC2)C1)C1=CC(=O)[N-]O1) `REAL250005045045.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045045 none O=C(NCCNC(=O)C1CC(C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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, 135, 103, 33, 33, 5, 33, 5, 5, 1, 1, 1, 1, 5, 201, 201, 201, 201, 201, 201, 201, 135, 135, 103, 103, 33, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38]) total number of confs: 761 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045045 none O=C(NCCNC(=O)C1CC(C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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, 23, 39, 98, 98, 98, 187, 187, 187, 201, 201, 187, 1, 1, 1, 1, 1, 1, 4, 23, 23, 39, 39, 98, 187, 187, 187, 187, 201, 201, 201, 201, 201, 187, 187, 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: 643 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045045 none O=C(NCCNC(=O)C1CC(C2CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [185, 184, 95, 62, 12, 12, 1, 12, 1, 1, 1, 1, 5, 5, 1, 184, 187, 187, 187, 187, 187, 185, 95, 95, 62, 62, 12, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 187] 201 rigid atoms, others: [36, 37, 6, 8, 9, 10, 11, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 38]) total number of confs: 699 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045045 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045045 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045045/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045045 Building REAL250005045046 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045046' /scratch/stefan/7916127/working/building/REAL250005045046 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045046 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045046/0 /scratch/stefan/7916127/working/building/REAL250005045046 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/163 `/scratch/stefan/7916127/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](NC=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045046.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045046 none CC(C)[C@H](NC=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 6, 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] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [128, 89, 127, 46, 89, 89, 108, 110, 46, 46, 19, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 128, 128, 128, 128, 128, 128, 128, 108, 110, 46, 19, 19, 11, 11, 4, 1] 130 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: 650 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045046 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045046 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045046/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045046 Building REAL250005045047 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045047' /scratch/stefan/7916127/working/building/REAL250005045047 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045047 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045047/0 /scratch/stefan/7916127/working/building/REAL250005045047 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/164 `/scratch/stefan/7916127/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045047.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045047 none CCSC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 149, 74, 74, 74, 28, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 74, 28, 28, 18, 18, 4, 1, 149, 149, 149, 149] 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: 698 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045047 none CCSC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 8, 8, 8, 44, 60, 140, 141, 140, 149, 149, 149, 149, 149, 1, 1, 11, 11, 11, 11, 11, 8, 44, 44, 60, 60, 141, 149, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 18, 19] set([0, 1, 5, 6, 7, 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: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045047 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045047 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045047/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045047 Building REAL250005045048 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045048' /scratch/stefan/7916127/working/building/REAL250005045048 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045048 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045048/0 /scratch/stefan/7916127/working/building/REAL250005045048 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/165 `/scratch/stefan/7916127/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045048.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045048 none CN(C)C(=O)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 150, 201, 150, 92, 92, 92, 33, 26, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 150, 150, 92, 33, 33, 26, 26, 10, 1] 201 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: 638 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045048 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045048 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045048/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045048 Building REAL250005045049 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045049' /scratch/stefan/7916127/working/building/REAL250005045049 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045049 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045049/0 /scratch/stefan/7916127/working/building/REAL250005045049 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/166 `/scratch/stefan/7916127/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045049.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045049 none C#CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', '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, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 81, 81, 81, 41, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 81, 41, 41, 26, 26, 4, 1, 201, 201, 201, 201] 201 rigid atoms, others: [9, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045049 none C#CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', '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, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 53, 92, 199, 201, 199, 201, 201, 201, 201, 201, 1, 1, 1, 7, 53, 53, 92, 92, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 27, 28, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045049 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045049 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045049/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045049 Building REAL250005045050 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045050' /scratch/stefan/7916127/working/building/REAL250005045050 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045050 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045050/0 /scratch/stefan/7916127/working/building/REAL250005045050 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/167 `/scratch/stefan/7916127/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CS1) `REAL250005045050.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045050 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 75, 75, 75, 37, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 75, 37, 37, 22, 22, 7, 1, 77] 77 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045050 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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, 4, 4, 4, 27, 43, 75, 75, 75, 77, 77, 77, 77, 77, 1, 1, 2, 2, 2, 4, 26, 26, 43, 43, 75, 77, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 279 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045050 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045050 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045050/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045050 Building REAL250005045051 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045051' /scratch/stefan/7916127/working/building/REAL250005045051 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045051 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045051/0 /scratch/stefan/7916127/working/building/REAL250005045051 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/168 `/scratch/stefan/7916127/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COCC1) `REAL250005045051.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045051 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 60, 84, 138, 138, 138, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 13, 60, 60, 84, 84, 138, 142, 1, 1, 1, 1, 1] 142 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 504 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045051 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [104, 104, 43, 30, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 104, 142, 142, 142, 142, 104, 43, 43, 30, 30, 11, 1, 142, 142, 142, 142, 142] 142 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 404 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045051 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045051 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045051/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045051 Building REAL250005045052 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045052' /scratch/stefan/7916127/working/building/REAL250005045052 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045052 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045052/0 /scratch/stefan/7916127/working/building/REAL250005045052 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/169 `/scratch/stefan/7916127/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CCCSC1)C1=CC(=O)[N-]O1) `REAL250005045052.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045052 none O=C(NCCNC(=O)C1=CCCSC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 33, 46, 106, 107, 106, 187, 187, 187, 187, 187, 1, 1, 1, 1, 1, 1, 9, 33, 33, 46, 46, 107, 187, 187, 187, 187, 187, 187, 187, 1] 187 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045052 none O=C(NCCNC(=O)C1=CCCSC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 5, 5, 14, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [178, 177, 100, 58, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 177, 187, 187, 187, 187, 187, 178, 100, 100, 58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 187] 187 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045052 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045052 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045052/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045052 Building REAL250005045053 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045053' /scratch/stefan/7916127/working/building/REAL250005045053 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045053 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045053/0 /scratch/stefan/7916127/working/building/REAL250005045053 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/170 `/scratch/stefan/7916127/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(F)=NN1) `REAL250005045053.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045053 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(F)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 15, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [9, 1, 9, 9, 35, 50, 83, 83, 83, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 9, 35, 35, 50, 50, 83, 91, 1, 1] 91 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045053 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(F)=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'F', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 15, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [75, 75, 37, 26, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 75, 91, 91, 91, 91, 91, 75, 37, 37, 26, 26, 11, 1, 91, 91] 91 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045053 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045053 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045053/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045053 Building REAL250005045054 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045054' /scratch/stefan/7916127/working/building/REAL250005045054 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045054 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045054/0 /scratch/stefan/7916127/working/building/REAL250005045054 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/171 `/scratch/stefan/7916127/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1C=CCC1)C1=CC(=O)[N-]O1) `REAL250005045054.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045054 none O=C(NCCNC(=O)C1C=CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 35, 48, 108, 108, 108, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 35, 35, 48, 48, 108, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 648 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: REAL250005045054 none O=C(NCCNC(=O)C1C=CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 186, 111, 69, 12, 12, 1, 12, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 187, 111, 111, 69, 69, 12, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 731 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045054 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045054 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045054/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045054 Building REAL250005045055 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045055' /scratch/stefan/7916127/working/building/REAL250005045055 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045055 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045055/0 /scratch/stefan/7916127/working/building/REAL250005045055 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/172 `/scratch/stefan/7916127/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCC(O)C1)C1=CC(=O)[N-]O1) `REAL250005045055.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045055 none O=C(NCCNC(=O)C1CCCC(O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 27, 42, 110, 110, 110, 201, 201, 200, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 27, 27, 42, 42, 110, 201, 201, 201, 201, 201, 200, 201, 201, 603, 201, 201, 1] 603 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: 1251 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045055 none O=C(NCCNC(=O)C1CCCC(O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 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] 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: [197, 197, 111, 75, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 197, 201, 201, 201, 201, 201, 197, 111, 111, 75, 75, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 1, 1, 201] 603 rigid atoms, others: [32, 33, 34, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 38]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045055 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045055 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045055/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045055 Building REAL250005045056 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045056' /scratch/stefan/7916127/working/building/REAL250005045056 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045056 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045056/0 /scratch/stefan/7916127/working/building/REAL250005045056 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/173 `/scratch/stefan/7916127/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045056.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045056 none CC1CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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, 156, 122, 122, 122, 58, 40, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 156, 156, 156, 156, 156, 156, 156, 156, 156, 122, 58, 58, 40, 40, 11, 1, 156, 156, 156, 156] 156 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: 480 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045056 none CC1CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 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, 1, 11, 11, 11, 61, 95, 142, 142, 142, 156, 156, 156, 156, 156, 1, 1, 2, 2, 2, 1, 1, 1, 1, 11, 61, 61, 95, 95, 142, 156, 1, 1, 1, 1] 156 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 38, 19, 20, 24, 25, 26, 27, 37, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045056 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045056 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045056/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045056 Building REAL250005045057 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045057' /scratch/stefan/7916127/working/building/REAL250005045057 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045057 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045057/0 /scratch/stefan/7916127/working/building/REAL250005045057 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/174 `/scratch/stefan/7916127/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045057.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045057 none CC(O)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 184, 201, 99, 184, 99, 99, 38, 24, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 184, 184, 184, 184, 99, 38, 38, 24, 24, 5, 1] 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]) total number of confs: 1420 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045057 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045057 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045057/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045057 Building REAL250005045058 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045058' /scratch/stefan/7916127/working/building/REAL250005045058 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045058 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045058/0 /scratch/stefan/7916127/working/building/REAL250005045058 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/175 `/scratch/stefan/7916127/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(O)CCOC1)C1=CC(=O)[N-]O1) `REAL250005045058.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045058 none O=C(NCCNC(=O)C1(O)CCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [8, 1, 8, 8, 29, 44, 102, 102, 102, 156, 156, 156, 156, 156, 1, 1, 1, 1, 1, 1, 8, 29, 29, 44, 44, 102, 468, 156, 156, 156, 156, 156, 156, 1] 468 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 997 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: REAL250005045058 none O=C(NCCNC(=O)C1(O)CCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [150, 149, 86, 55, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 149, 156, 156, 156, 156, 156, 150, 86, 86, 55, 55, 11, 6, 1, 1, 1, 1, 1, 1, 156] 468 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 33, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 596 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045058 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045058 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045058/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045058 Building REAL250005045059 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045059' /scratch/stefan/7916127/working/building/REAL250005045059 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045059 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045059/0 /scratch/stefan/7916127/working/building/REAL250005045059 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/176 `/scratch/stefan/7916127/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1[N-]C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC1=O) `REAL250005045059.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045059 none CN1[N-]C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 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, 35, 35, 35, 35, 35, 21, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 21, 21, 15, 15, 7, 1, 35] 35 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]) 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: REAL250005045059 none CN1[N-]C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'N.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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 14, 17, 27, 27, 27, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 4, 14, 14, 17, 17, 27, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045059 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045059 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045059/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045059 Building REAL250005045060 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045060' /scratch/stefan/7916127/working/building/REAL250005045060 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045060 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045060/0 /scratch/stefan/7916127/working/building/REAL250005045060 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/177 `/scratch/stefan/7916127/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045060.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045060 none C=C1CC1C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 99, 99, 45, 29, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 99, 45, 45, 29, 29, 7, 1] 201 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]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045060 none C=C1CC1C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 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, 71, 110, 189, 193, 189, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 71, 71, 110, 110, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045060 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045060 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045060/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045060 Building REAL250005045061 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045061' /scratch/stefan/7916127/working/building/REAL250005045061 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045061 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045061/0 /scratch/stefan/7916127/working/building/REAL250005045061 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/178 `/scratch/stefan/7916127/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC=CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045061.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045061 none O=C(CC1CC=CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 1, 1, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 163, 201, 201, 201, 201, 34, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 201, 201, 59, 34, 34, 23, 23, 4, 1] 201 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: 794 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045061 none O=C(CC1CC=CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 1, 1, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 32, 32, 120, 142, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 32, 120, 120, 142, 142, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045061 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045061 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045061/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045061 Building REAL250005045062 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045062' /scratch/stefan/7916127/working/building/REAL250005045062 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045062 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045062/0 /scratch/stefan/7916127/working/building/REAL250005045062 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/179 `/scratch/stefan/7916127/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=[NH2+])SCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045062.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045062 none NC(=[NH2+])SCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.cat', 'N.pl3', 'H', 'H', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 6, 6, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 4, 7, 7, 7, 7, 7, 6, 4, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 7, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 9, 9, 9, 7, 7, 2, 1] 15 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045062 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045062 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045062/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045062 Building REAL250005045063 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045063' /scratch/stefan/7916127/working/building/REAL250005045063 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045063 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045063/0 /scratch/stefan/7916127/working/building/REAL250005045063 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/180 `/scratch/stefan/7916127/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC[N+](=O)[O-])NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045063.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045063 none O=C(CCC[N+](=O)[O-])NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 8, 11, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 147, 149, 201, 201, 201, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 147, 147, 181, 181, 192, 192, 59, 23, 23, 14, 14, 4, 1] 201 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]) total number of confs: 1029 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045063 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045063 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045063/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045063 Building REAL250005045064 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045064' /scratch/stefan/7916127/working/building/REAL250005045064 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045064 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045064/0 /scratch/stefan/7916127/working/building/REAL250005045064 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/181 `/scratch/stefan/7916127/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CF)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045064.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045064 none CC(CF)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 85, 188, 201, 85, 85, 36, 21, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 201, 201, 85, 36, 36, 21, 21, 5, 1] 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]) total number of confs: 822 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045064 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045064 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045064/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045064 Building REAL250005045065 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045065' /scratch/stefan/7916127/working/building/REAL250005045065 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045065 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045065/0 /scratch/stefan/7916127/working/building/REAL250005045065 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/182 `/scratch/stefan/7916127/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1COC[C@H]1O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045065.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045065 none O=C(C[C@@H]1COC[C@H]1O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 12, 5, 5, 7, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 179, 201, 201, 201, 201, 201, 201, 201, 32, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 180, 180, 201, 201, 201, 201, 603, 70, 32, 32, 18, 18, 4, 1] 603 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: 1378 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: REAL250005045065 none O=C(C[C@@H]1COC[C@H]1O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 12, 5, 5, 7, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 104, 128, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 3, 34, 104, 104, 128, 128, 201, 201] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 753 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045065 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045065 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045065/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045065 Building REAL250005045066 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045066' /scratch/stefan/7916127/working/building/REAL250005045066 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045066 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045066/0 /scratch/stefan/7916127/working/building/REAL250005045066 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/183 `/scratch/stefan/7916127/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1=NC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045066.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045066 none O=C(C=CC1=NC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 8, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 149, 149, 201, 201, 201, 201, 41, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 99, 41, 41, 26, 26, 7, 1] 201 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]) total number of confs: 578 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045066 none O=C(C=CC1=NC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 8, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 6, 6, 1, 1, 1, 1, 1, 1, 32, 32, 98, 131, 197, 197, 197, 201, 201, 201, 201, 201, 6, 6, 1, 1, 32, 98, 98, 131, 131, 197, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045066 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045066 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045066/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045066 Building REAL250005045067 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045067' /scratch/stefan/7916127/working/building/REAL250005045067 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045067 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045067/0 /scratch/stefan/7916127/working/building/REAL250005045067 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/184 `/scratch/stefan/7916127/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC1CCC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045067.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045067 none CC(CC1CCC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 41, 126, 162, 201, 201, 201, 41, 41, 26, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 162, 162, 201, 201, 201, 201, 201, 201, 201, 41, 26, 26, 16, 16, 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: 878 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045067 none CC(CC1CCC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 1, 1, 14, 48, 48, 48, 117, 137, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 48, 117, 117, 137, 137, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 27, 28, 29, 30, 31] set([0, 1, 7, 8, 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: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045067 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045067 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045067/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045067 Building REAL250005045068 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045068' /scratch/stefan/7916127/working/building/REAL250005045068 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045068 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045068/0 /scratch/stefan/7916127/working/building/REAL250005045068 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/185 `/scratch/stefan/7916127/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045068.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045068 none CC1(C)C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 69, 69, 69, 36, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 69, 36, 36, 24, 24, 9, 1, 85, 85] 85 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: 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: REAL250005045068 none CC1(C)C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 32, 45, 79, 79, 79, 85, 85, 85, 85, 85, 1, 2, 2, 2, 2, 2, 2, 1, 8, 32, 32, 45, 45, 79, 85, 1, 1] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 302 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045068 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045068 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045068/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045068 Building REAL250005045069 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045069' /scratch/stefan/7916127/working/building/REAL250005045069 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045069 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045069/0 /scratch/stefan/7916127/working/building/REAL250005045069 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/186 `/scratch/stefan/7916127/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NNC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045069.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045069 none O=C(CCC1=NNC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 133, 165, 201, 201, 201, 201, 31, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 133, 133, 165, 165, 201, 201, 201, 65, 31, 31, 20, 20, 4, 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: 770 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045069 none O=C(CCC1=NNC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 14, 8, 1, 1, 1, 1, 1, 1, 59, 59, 147, 163, 201, 201, 201, 201, 201, 201, 201, 201, 14, 14, 8, 8, 1, 1, 1, 59, 147, 147, 163, 163, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045069 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045069 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045069/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045069 Building REAL250005045070 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045070' /scratch/stefan/7916127/working/building/REAL250005045070 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045070 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045070/0 /scratch/stefan/7916127/working/building/REAL250005045070 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/187 `/scratch/stefan/7916127/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(O)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045070.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045070 none CC1(C)CC(O)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7] 1 hydrogens need rotated 519 conformations in input total number of sets (complete confs): 519 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 117, 173, 117, 117, 52, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 173, 173, 173, 173, 173, 173, 173, 173, 173, 519, 117, 52, 52, 34, 34, 9, 1, 173, 173] 519 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: 1103 number of broken/clashed sets: 173 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045070 none CC1(C)CC(O)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 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, 7] 1 hydrogens need rotated 519 conformations in input total number of sets (complete confs): 519 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 58, 98, 161, 161, 161, 173, 173, 173, 173, 173, 1, 2, 2, 2, 2, 2, 2, 1, 1, 3, 10, 58, 58, 98, 98, 161, 173, 1, 1] 519 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 38, 20, 27, 28, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 652 number of broken/clashed sets: 173 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045070 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045070 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045070/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045070 Building REAL250005045071 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045071' /scratch/stefan/7916127/working/building/REAL250005045071 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045071 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045071/0 /scratch/stefan/7916127/working/building/REAL250005045071 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/188 `/scratch/stefan/7916127/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(C2CC2)CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045071.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045071 none O=C(CC1(C2CC2)CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 8, 1, 1, 1, 1, 8, 8, 67, 67, 110, 117, 201, 201, 201, 201, 201, 201, 201, 201, 20, 20, 1, 1, 1, 1, 1, 8, 8, 8, 8, 67, 110, 110, 117, 117, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 23, 24, 25, 26, 27] set([0, 1, 2, 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, 37, 38]) total number of confs: 717 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045071 none O=C(CC1(C2CC2)CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 124, 169, 201, 201, 169, 169, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 201, 169, 169, 169, 169, 28, 23, 23, 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: 769 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045071 none O=C(CC1(C2CC2)CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 8, 1, 1, 1, 8, 8, 1, 1, 37, 37, 71, 79, 165, 165, 165, 169, 169, 169, 169, 169, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 37, 71, 71, 79, 79, 165, 169] 201 rigid atoms, others: [2, 3, 4, 7, 8, 28, 29, 30, 31] set([0, 1, 5, 6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 582 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045071 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045071 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045071/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045071 Building REAL250005045072 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045072' /scratch/stefan/7916127/working/building/REAL250005045072 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045072 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045072/0 /scratch/stefan/7916127/working/building/REAL250005045072 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/189 `/scratch/stefan/7916127/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CC1(F)F)C1=CC(=O)[N-]O1) `REAL250005045072.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045072 none O=C(NCCNC(=O)[C@@H]1CC1(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 31, 49, 118, 118, 118, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 31, 31, 50, 50, 118, 201, 201, 1] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045072 none O=C(NCCNC(=O)[C@@H]1CC1(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 194, 111, 72, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 195, 111, 111, 72, 72, 13, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045072 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045072 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045072/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045072 Building REAL250005045073 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045073' /scratch/stefan/7916127/working/building/REAL250005045073 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045073 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045073/0 /scratch/stefan/7916127/working/building/REAL250005045073 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/190 `/scratch/stefan/7916127/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1C2C3CC1CC32)C1=CC(=O)[N-]O1) `REAL250005045073.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045073 none O=C(NCCNC(=O)C1C2C3CC1CC32)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 29, 41, 100, 100, 100, 129, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 10, 29, 29, 41, 41, 100, 129, 129, 129, 129, 129, 129, 129, 129, 129, 1] 129 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: 434 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045073 none O=C(NCCNC(=O)C1C2C3CC1CC32)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 67, 39, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 122, 129, 129, 129, 129, 129, 122, 67, 67, 39, 39, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129] 129 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 457 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045073 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045073 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045073/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045073 Building REAL250005045074 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045074' /scratch/stefan/7916127/working/building/REAL250005045074 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045074 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045074/0 /scratch/stefan/7916127/working/building/REAL250005045074 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/191 `/scratch/stefan/7916127/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H](O)C1CCCC1)C1=CC(=O)[N-]O1) `REAL250005045074.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045074 none O=C(NCCNC(=O)[C@@H](O)C1CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [4, 1, 4, 4, 18, 27, 76, 76, 76, 185, 185, 185, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 18, 18, 27, 27, 76, 555, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 603 rigid atoms, others: [1, 38, 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, 33, 34, 35, 36, 37]) total number of confs: 1329 number of broken/clashed sets: 90 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045074 none O=C(NCCNC(=O)[C@@H](O)C1CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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, 119, 97, 26, 26, 5, 26, 1, 5, 5, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 119, 119, 97, 97, 26, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 603 rigid atoms, others: [32, 33, 34, 35, 36, 37, 8, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38]) total number of confs: 753 number of broken/clashed sets: 90 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045074 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045074 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045074/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045074 Building REAL250005045075 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045075' /scratch/stefan/7916127/working/building/REAL250005045075 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045075 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045075/0 /scratch/stefan/7916127/working/building/REAL250005045075 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/192 `/scratch/stefan/7916127/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045075.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045075 none CC(=O)NCCC(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 200, 164, 152, 61, 61, 61, 29, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 165, 165, 153, 153, 61, 29, 29, 18, 18, 4, 1] 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]) total number of confs: 819 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045075 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045075 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045075/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045075 Building REAL250005045076 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045076' /scratch/stefan/7916127/working/building/REAL250005045076 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045076 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045076/0 /scratch/stefan/7916127/working/building/REAL250005045076 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/193 `/scratch/stefan/7916127/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNC(=O)N1) `REAL250005045076.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045076 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 6, 4, 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: [10, 1, 10, 10, 44, 64, 111, 111, 111, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 10, 44, 44, 64, 64, 111, 117, 1, 1, 1] 117 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045076 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 4, 7, 6, 4, 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: [73, 73, 33, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 73, 117, 117, 117, 117, 117, 73, 33, 33, 24, 24, 9, 1, 117, 117, 117] 117 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]) total number of confs: 322 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045076 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045076 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045076/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045076 Building REAL250005045077 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045077' /scratch/stefan/7916127/working/building/REAL250005045077 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045077 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045077/0 /scratch/stefan/7916127/working/building/REAL250005045077 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/194 `/scratch/stefan/7916127/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045077.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045077 none CC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 117, 117, 117, 46, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 46, 46, 30, 30, 8, 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: 637 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: REAL250005045077 none CC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 60, 99, 194, 194, 194, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 60, 60, 99, 99, 194, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 721 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045077 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045077 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045077/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045077 Building REAL250005045078 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045078' /scratch/stefan/7916127/working/building/REAL250005045078 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045078 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045078/0 /scratch/stefan/7916127/working/building/REAL250005045078 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/195 `/scratch/stefan/7916127/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045078.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045078 none CC1CCC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 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, 120, 201, 120, 122, 51, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 51, 51, 34, 34, 11, 1, 201, 201] 201 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: 677 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: REAL250005045078 none CC1CCC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 37, 62, 180, 182, 180, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 6, 37, 37, 62, 62, 182, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 20, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 645 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045078 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045078 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045078/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045078 Building REAL250005045079 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045079' /scratch/stefan/7916127/working/building/REAL250005045079 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045079 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045079/0 /scratch/stefan/7916127/working/building/REAL250005045079 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/196 `/scratch/stefan/7916127/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045079.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045079 none C=C(C)CC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 113, 113, 113, 47, 28, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 113, 47, 47, 28, 28, 6, 1] 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]) total number of confs: 809 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045079 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045079 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045079/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045079 Building REAL250005045080 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045080' /scratch/stefan/7916127/working/building/REAL250005045080 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045080 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045080/0 /scratch/stefan/7916127/working/building/REAL250005045080 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/197 `/scratch/stefan/7916127/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045080.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045080 none CC1=CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 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, 122, 122, 123, 57, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 57, 57, 37, 37, 11, 1, 201, 201, 201, 201] 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: 671 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: REAL250005045080 none CC1=CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 12, 12, 12, 63, 108, 180, 184, 180, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 63, 63, 108, 108, 184, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 38, 19, 20, 24, 25, 26, 27, 37, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 756 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045080 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045080 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045080/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045080 Building REAL250005045081 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045081' /scratch/stefan/7916127/working/building/REAL250005045081 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045081 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045081/0 /scratch/stefan/7916127/working/building/REAL250005045081 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/198 `/scratch/stefan/7916127/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045081.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045081 none CCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 130, 63, 63, 63, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 130, 130, 63, 23, 23, 14, 14, 4, 1] 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]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045081 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045081 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045081/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045081 Building REAL250005045082 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045082' /scratch/stefan/7916127/working/building/REAL250005045082 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045082 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045082/0 /scratch/stefan/7916127/working/building/REAL250005045082 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/199 `/scratch/stefan/7916127/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045082.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045082 none CC(C)=C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 115, 161, 115, 115, 54, 34, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 161, 161, 161, 115, 54, 54, 34, 34, 9, 1] 161 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: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045082 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045082 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045082/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045082 Building REAL250005045083 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045083' /scratch/stefan/7916127/working/building/REAL250005045083 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045083 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045083/0 /scratch/stefan/7916127/working/building/REAL250005045083 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/200 `/scratch/stefan/7916127/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C(F)(F)C(F)F)C1=CC(=O)[N-]O1) `REAL250005045083.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045083 none O=C(NCCNC(=O)C(F)(F)C(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'F', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 15, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 12, 11, 29, 34, 93, 93, 93, 193, 193, 193, 201, 201, 1, 1, 1, 1, 1, 1, 12, 29, 29, 34, 34, 93, 201, 1] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 771 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045083 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045083 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045083/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045083 Building REAL250005045084 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045084' /scratch/stefan/7916127/working/building/REAL250005045084 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045084 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045084/0 /scratch/stefan/7916127/working/building/REAL250005045084 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/201 `/scratch/stefan/7916127/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045084.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045084 none CCCC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [200, 194, 140, 95, 140, 95, 95, 37, 23, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 195, 195, 140, 420, 95, 37, 37, 23, 23, 4, 1] 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]) total number of confs: 1284 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045084 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045084 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045084/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045084 Building REAL250005045085 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045085' /scratch/stefan/7916127/working/building/REAL250005045085 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045085 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045085/0 /scratch/stefan/7916127/working/building/REAL250005045085 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/202 `/scratch/stefan/7916127/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045085.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045085 none CCCCC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 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, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [198, 190, 177, 102, 64, 102, 64, 64, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 190, 188, 180, 180, 102, 306, 64, 23, 23, 14, 14, 4, 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: 1246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045085 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045085 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045085/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045085 Building REAL250005045086 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045086' /scratch/stefan/7916127/working/building/REAL250005045086 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045086 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045086/0 /scratch/stefan/7916127/working/building/REAL250005045086 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/203 `/scratch/stefan/7916127/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)O) `REAL250005045086.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045086 none COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)O 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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 6, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [173, 154, 94, 94, 94, 32, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 155, 200, 200, 173, 173, 173, 156, 94, 32, 32, 22, 22, 6, 1, 200, 200, 200, 200, 600] 603 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: 1477 number of broken/clashed sets: 73 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045086 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045086 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045086/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045086 Building REAL250005045087 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045087' /scratch/stefan/7916127/working/building/REAL250005045087 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045087 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045087/0 /scratch/stefan/7916127/working/building/REAL250005045087 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/204 `/scratch/stefan/7916127/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CSC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045087.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045087 none O=C(CSC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 14, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 107, 154, 201, 201, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 107, 107, 201, 201, 201, 201, 201, 47, 19, 19, 10, 10, 2, 1] 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]) total number of confs: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045087 none O=C(CSC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 14, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 30, 6, 1, 1, 1, 1, 77, 77, 137, 140, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 1, 1, 1, 1, 1, 77, 137, 137, 140, 140, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 21, 22, 23, 24, 25] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045087 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045087 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045087/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045087 Building REAL250005045088 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045088' /scratch/stefan/7916127/working/building/REAL250005045088 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045088 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045088/0 /scratch/stefan/7916127/working/building/REAL250005045088 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/205 `/scratch/stefan/7916127/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045088.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045088 none O=C(CCCC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 102, 110, 141, 201, 201, 201, 26, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 102, 102, 115, 115, 141, 141, 201, 201, 201, 201, 201, 201, 201, 28, 26, 26, 18, 18, 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: 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: REAL250005045088 none O=C(CCCC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 10, 6, 1, 1, 1, 1, 1, 72, 72, 122, 122, 201, 201, 201, 201, 201, 201, 201, 201, 20, 20, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 72, 122, 122, 122, 122, 201, 201] 201 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 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: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045088 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045088 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045088/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045088 Building REAL250005045089 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045089' /scratch/stefan/7916127/working/building/REAL250005045089 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045089 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045089/0 /scratch/stefan/7916127/working/building/REAL250005045089 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/206 `/scratch/stefan/7916127/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045089.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045089 none CCC(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 155, 187, 76, 76, 76, 31, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 187, 561, 155, 155, 76, 31, 31, 20, 20, 4, 1] 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]) total number of confs: 1451 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045089 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045089 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045089/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045089 Building REAL250005045090 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045090' /scratch/stefan/7916127/working/building/REAL250005045090 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045090 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045090/0 /scratch/stefan/7916127/working/building/REAL250005045090 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/207 `/scratch/stefan/7916127/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(Cl)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045090.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045090 none CC(Cl)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'Cl', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 16, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 122, 122, 122, 62, 38, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 122, 62, 62, 38, 38, 11, 1] 178 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]) total number of confs: 613 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045090 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045090 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045090/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045090 Building REAL250005045091 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045091' /scratch/stefan/7916127/working/building/REAL250005045091 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045091 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045091/0 /scratch/stefan/7916127/working/building/REAL250005045091 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/208 `/scratch/stefan/7916127/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)NCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045091.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045091 none CN1C(=O)NCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 123, 123, 123, 57, 39, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 147, 123, 57, 57, 39, 39, 10, 1] 147 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: 496 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045091 none CN1C(=O)NCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 39, 65, 136, 136, 136, 147, 147, 147, 147, 147, 2, 2, 2, 1, 1, 1, 1, 8, 39, 39, 65, 65, 136, 147] 147 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045091 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045091 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045091/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045091 Building REAL250005045092 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045092' /scratch/stefan/7916127/working/building/REAL250005045092 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045092 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045092/0 /scratch/stefan/7916127/working/building/REAL250005045092 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/209 `/scratch/stefan/7916127/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045092.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045092 none CCC(F)(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 190, 80, 192, 192, 80, 80, 28, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 80, 28, 28, 17, 17, 4, 1] 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]) total number of confs: 948 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045092 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045092 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045092/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045092 Building REAL250005045093 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045093' /scratch/stefan/7916127/working/building/REAL250005045093 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045093 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045093/0 /scratch/stefan/7916127/working/building/REAL250005045093 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/210 `/scratch/stefan/7916127/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCCC1F)C1=CC(=O)[N-]O1) `REAL250005045093.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045093 none O=C(NCCNC(=O)C1CCCCC1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 30, 48, 124, 124, 124, 201, 201, 200, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 30, 30, 48, 48, 124, 201, 201, 201, 201, 201, 201, 200, 201, 201, 201, 1] 201 rigid atoms, others: [1, 37, 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]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045093 none O=C(NCCNC(=O)C1CCCCC1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens 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, 116, 80, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 194, 201, 201, 201, 201, 201, 194, 116, 116, 80, 80, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 736 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045093 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045093 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045093/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045093 Building REAL250005045094 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045094' /scratch/stefan/7916127/working/building/REAL250005045094 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045094 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045094/0 /scratch/stefan/7916127/working/building/REAL250005045094 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/211 `/scratch/stefan/7916127/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1F) `REAL250005045094.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045094 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1F 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', 'F', '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, 15, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 99, 99, 99, 52, 35, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 99, 52, 52, 35, 35, 9, 1, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31]) total number of confs: 664 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045094 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1F 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', 'F', '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, 15, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 47, 93, 190, 191, 190, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 7, 47, 47, 93, 93, 191, 201, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 16, 17, 18, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045094 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045094 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045094/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045094 Building REAL250005045095 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045095' /scratch/stefan/7916127/working/building/REAL250005045095 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045095 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045095/0 /scratch/stefan/7916127/working/building/REAL250005045095 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/212 `/scratch/stefan/7916127/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1C[C@@H](O)C1)C1=CC(=O)[N-]O1) `REAL250005045095.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045095 none O=C(NCCNC(=O)[C@H]1C[C@@H](O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 35, 58, 119, 119, 119, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 35, 35, 58, 58, 119, 201, 201, 603, 201, 201, 1] 603 rigid atoms, others: [32, 1, 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]) total number of confs: 1264 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: REAL250005045095 none O=C(NCCNC(=O)[C@H]1C[C@@H](O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 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, 195, 109, 66, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 195, 109, 109, 66, 66, 13, 1, 1, 6, 1, 1, 201] 603 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29]) total number of confs: 744 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045095 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045095 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045095/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045095 Building REAL250005045096 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045096' /scratch/stefan/7916127/working/building/REAL250005045096 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045096 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045096/0 /scratch/stefan/7916127/working/building/REAL250005045096 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/213 `/scratch/stefan/7916127/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045096.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045096 none CC1(C)CC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 173, 70, 70, 70, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 174, 70, 30, 30, 19, 19, 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: 782 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045096 none CC1(C)CC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 5, 36, 36, 36, 112, 130, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 36, 112, 112, 130, 130, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045096 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045096 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045096/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045096 Building REAL250005045097 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045097' /scratch/stefan/7916127/working/building/REAL250005045097 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045097 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045097/0 /scratch/stefan/7916127/working/building/REAL250005045097 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/214 `/scratch/stefan/7916127/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045097.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045097 none CCCCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 189, 142, 89, 89, 89, 23, 23, 23, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 189, 189, 142, 142, 89, 89, 89, 89, 89, 89, 23, 23, 23, 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: 922 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045097 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045097 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045097/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045097 Building REAL250005045098 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045098' /scratch/stefan/7916127/working/building/REAL250005045098 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045098 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045098/0 /scratch/stefan/7916127/working/building/REAL250005045098 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/215 `/scratch/stefan/7916127/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(NC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045098.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045098 none CC(NC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 4, 6, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 95, 195, 201, 201, 201, 95, 95, 39, 28, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 195, 193, 195, 195, 201, 201, 201, 95, 39, 39, 28, 28, 9, 1] 201 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]) total number of confs: 794 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045098 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045098 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045098/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045098 Building REAL250005045099 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045099' /scratch/stefan/7916127/working/building/REAL250005045099 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045099 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045099/0 /scratch/stefan/7916127/working/building/REAL250005045099 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/216 `/scratch/stefan/7916127/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(O)CCOCC1)C1=CC(=O)[N-]O1) `REAL250005045099.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045099 none O=C(NCCNC(=O)C1(O)CCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [11, 1, 11, 11, 30, 41, 99, 99, 99, 157, 157, 157, 157, 157, 157, 1, 1, 1, 1, 1, 1, 11, 30, 30, 41, 41, 99, 471, 157, 157, 157, 157, 157, 157, 157, 157, 1] 471 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: 994 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045099 none O=C(NCCNC(=O)C1(O)CCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 12, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [148, 148, 87, 63, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 148, 157, 157, 157, 157, 157, 148, 87, 87, 63, 63, 13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 157] 471 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045099 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045099 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045099/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045099 Building REAL250005045100 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045100' /scratch/stefan/7916127/working/building/REAL250005045100 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045100 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045100/0 /scratch/stefan/7916127/working/building/REAL250005045100 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/217 `/scratch/stefan/7916127/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)C#CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045100.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045100 none CN(C)C(=O)C#CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 6, 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] 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: [39, 35, 53, 53, 53, 53, 53, 53, 53, 35, 26, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 35, 35, 26, 26, 9, 1] 53 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]) total number of confs: 350 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045100 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045100 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045100/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045100 Building REAL250005045101 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045101' /scratch/stefan/7916127/working/building/REAL250005045101 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045101 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045101/0 /scratch/stefan/7916127/working/building/REAL250005045101 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/218 `/scratch/stefan/7916127/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045101.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045101 none C=C(C)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 102, 40, 40, 40, 30, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 153, 153, 103, 103, 40, 30, 30, 20, 20, 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: 994 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045101 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045101 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045101/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045101 Building REAL250005045102 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045102' /scratch/stefan/7916127/working/building/REAL250005045102 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045102 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045102/0 /scratch/stefan/7916127/working/building/REAL250005045102 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/219 `/scratch/stefan/7916127/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1C) `REAL250005045102.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045102 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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: [122, 122, 122, 80, 80, 80, 37, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 122, 122, 80, 37, 37, 22, 22, 7, 1, 122, 122, 122] 122 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: 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: REAL250005045102 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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, 8, 38, 60, 114, 116, 116, 122, 122, 122, 122, 122, 1, 1, 1, 2, 2, 2, 8, 38, 38, 60, 60, 116, 122, 2, 2, 2] 122 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045102 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045102 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045102/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045102 Building REAL250005045103 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045103' /scratch/stefan/7916127/working/building/REAL250005045103 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045103 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045103/0 /scratch/stefan/7916127/working/building/REAL250005045103 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/220 `/scratch/stefan/7916127/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC(F)C1) `REAL250005045103.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045103 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC(F)C1 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', 'F', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 126, 126, 126, 47, 30, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 126, 47, 47, 30, 30, 8, 1, 201, 201, 201, 201, 201] 201 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]) total number of confs: 656 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: REAL250005045103 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC(F)C1 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', 'F', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 15, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7] 0 hydrogens 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, 6, 6, 6, 44, 80, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 6, 44, 44, 80, 80, 195, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 32, 34, 16, 17, 18, 19, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 684 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045103 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045103 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045103/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045103 Building REAL250005045104 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045104' /scratch/stefan/7916127/working/building/REAL250005045104 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045104 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045104/0 /scratch/stefan/7916127/working/building/REAL250005045104 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/221 `/scratch/stefan/7916127/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045104.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045104 none CCC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 137, 137, 137, 137, 93, 93, 93, 35, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 137, 137, 93, 35, 35, 20, 20, 5, 1, 137] 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]) 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: REAL250005045104 none CCC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 11, 11, 11, 43, 61, 135, 135, 135, 137, 137, 137, 137, 137, 1, 9, 9, 9, 9, 9, 1, 1, 11, 43, 43, 61, 61, 135, 137, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 35, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 488 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045104 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045104 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045104/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045104 Building REAL250005045105 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045105' /scratch/stefan/7916127/working/building/REAL250005045105 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045105 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045105/0 /scratch/stefan/7916127/working/building/REAL250005045105 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/222 `/scratch/stefan/7916127/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C#CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045105.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045105 none O=C(C#CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 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, 54, 54, 54, 54, 54, 54, 30, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 30, 30, 20, 20, 7, 1] 54 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: 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: REAL250005045105 none O=C(C#CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 17, 50, 50, 50, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 50, 54] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28] set([32, 33, 34, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045105 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045105 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045105/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045105 Building REAL250005045106 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045106' /scratch/stefan/7916127/working/building/REAL250005045106 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045106 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045106/0 /scratch/stefan/7916127/working/building/REAL250005045106 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/223 `/scratch/stefan/7916127/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045106.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045106 none C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 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', 'N.am', 'C.2', 'O.2', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 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, 102, 201, 102, 102, 48, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 102, 48, 48, 29, 29, 6, 1] 201 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]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045106 none C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 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', 'N.am', 'C.2', 'O.2', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 66, 111, 189, 189, 189, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 66, 66, 111, 111, 189, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045106 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045106 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045106/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045106 Building REAL250005045107 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045107' /scratch/stefan/7916127/working/building/REAL250005045107 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045107 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045107/0 /scratch/stefan/7916127/working/building/REAL250005045107 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/224 `/scratch/stefan/7916127/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045107.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045107 none CNC(=O)NC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 172, 178, 143, 83, 143, 83, 83, 36, 26, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 172, 143, 143, 143, 143, 83, 36, 36, 26, 26, 9, 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: 774 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045107 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045107 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045107/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045107 Building REAL250005045108 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045108' /scratch/stefan/7916127/working/building/REAL250005045108 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045108 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045108/0 /scratch/stefan/7916127/working/building/REAL250005045108 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/225 `/scratch/stefan/7916127/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045108.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045108 none CCN1C=NN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 134, 134, 134, 134, 134, 128, 128, 128, 42, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 134, 128, 42, 42, 28, 28, 7, 1] 201 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]) 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: REAL250005045108 none CCN1C=NN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 45, 128, 128, 128, 134, 134, 134, 134, 134, 6, 6, 6, 6, 6, 1, 6, 24, 24, 45, 45, 128, 134] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 446 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045108 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045108 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045108/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045108 Building REAL250005045109 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045109' /scratch/stefan/7916127/working/building/REAL250005045109 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045109 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045109/0 /scratch/stefan/7916127/working/building/REAL250005045109 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/226 `/scratch/stefan/7916127/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(C2CCC2)CC1)C1=CC(=O)[N-]O1) `REAL250005045109.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045109 none O=C(NCCNC(=O)C1(C2CCC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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, 117, 91, 21, 21, 9, 21, 1, 1, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201, 201, 117, 117, 91, 91, 21, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 201] 201 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38]) total number of confs: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045109 none O=C(NCCNC(=O)C1(C2CCC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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, 17, 28, 80, 80, 80, 135, 201, 201, 201, 135, 135, 1, 1, 1, 1, 1, 1, 4, 17, 17, 28, 28, 80, 201, 201, 201, 201, 201, 201, 201, 135, 135, 135, 135, 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: 695 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045109 none O=C(NCCNC(=O)C1(C2CCC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [121, 121, 35, 24, 5, 5, 1, 5, 1, 1, 9, 9, 9, 1, 1, 121, 135, 135, 135, 135, 135, 121, 35, 35, 24, 24, 5, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 135] 201 rigid atoms, others: [34, 35, 36, 37, 6, 8, 9, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 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: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045109 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045109 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045109/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045109 Building REAL250005045110 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045110' /scratch/stefan/7916127/working/building/REAL250005045110 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045110 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045110/0 /scratch/stefan/7916127/working/building/REAL250005045110 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/227 `/scratch/stefan/7916127/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C1=CC(=O)[N-]O1) `REAL250005045110.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045110 none O=C(NCCNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 43, 106, 106, 106, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 29, 29, 43, 43, 106, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 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]) total number of confs: 646 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: REAL250005045110 none O=C(NCCNC(=O)[C@@H]1CC[C@@H]2C[C@@H]21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 7, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 193, 117, 71, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 194, 117, 117, 71, 71, 13, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 774 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045110 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045110 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045110/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045110 Building REAL250005045111 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045111' /scratch/stefan/7916127/working/building/REAL250005045111 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045111 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045111/0 /scratch/stefan/7916127/working/building/REAL250005045111 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/228 `/scratch/stefan/7916127/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1COC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045111.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045111 none O=C(COC1COC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 126, 164, 201, 201, 201, 21, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 126, 126, 201, 201, 201, 201, 201, 66, 21, 21, 13, 13, 4, 1] 201 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]) total number of confs: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045111 none O=C(COC1COC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 24, 6, 1, 1, 1, 1, 1, 57, 57, 121, 140, 201, 201, 201, 201, 201, 201, 201, 201, 24, 24, 1, 1, 1, 1, 1, 57, 121, 121, 140, 140, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 22, 23, 24, 25, 26] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045111 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045111 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045111/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045111 Building REAL250005045112 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045112' /scratch/stefan/7916127/working/building/REAL250005045112 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045112 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045112/0 /scratch/stefan/7916127/working/building/REAL250005045112 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/229 `/scratch/stefan/7916127/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@]2(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)C[C@H]12) `REAL250005045112.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045112 none C[C@@H]1C[C@]2(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 99, 99, 99, 48, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 99, 49, 49, 29, 29, 6, 1, 201, 201] 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: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045112 none C[C@@H]1C[C@]2(C(=O)NCCNC(=O)C3=CC(=O)[N-]O3)C[C@H]12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 46, 89, 186, 187, 186, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 7, 46, 46, 89, 89, 187, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045112 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045112 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045112/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045112 Building REAL250005045113 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045113' /scratch/stefan/7916127/working/building/REAL250005045113 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045113 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045113/0 /scratch/stefan/7916127/working/building/REAL250005045113 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/230 `/scratch/stefan/7916127/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045113.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045113 none CNC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 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] 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: [122, 122, 99, 122, 65, 65, 65, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 122, 122, 122, 122, 99, 99, 65, 25, 25, 16, 16, 4, 1] 122 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]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045113 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045113 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045113/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045113 Building REAL250005045114 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045114' /scratch/stefan/7916127/working/building/REAL250005045114 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045114 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045114/0 /scratch/stefan/7916127/working/building/REAL250005045114 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/231 `/scratch/stefan/7916127/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OC1COC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045114.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045114 none CC(OC1COC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens 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, 64, 143, 172, 201, 201, 201, 64, 64, 24, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 201, 201, 201, 201, 201, 64, 24, 24, 14, 14, 4, 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: 750 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045114 none CC(OC1COC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 19, 58, 58, 58, 138, 159, 201, 201, 201, 201, 201, 201, 201, 201, 19, 19, 19, 19, 1, 1, 1, 1, 1, 58, 138, 138, 159, 159, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 25, 26, 27, 28, 29] set([0, 1, 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: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045114 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045114 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045114/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045114 Building REAL250005045115 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045115' /scratch/stefan/7916127/working/building/REAL250005045115 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045115 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045115/0 /scratch/stefan/7916127/working/building/REAL250005045115 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/232 `/scratch/stefan/7916127/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045115.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045115 none CN1C(=O)CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 200, 200, 200, 134, 134, 135, 51, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 200, 200, 200, 200, 200, 201, 200, 200, 135, 51, 51, 34, 34, 11, 1] 201 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: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045115 none CN1C(=O)CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 55, 92, 190, 191, 190, 201, 201, 201, 201, 200, 2, 2, 2, 1, 1, 1, 1, 1, 10, 55, 55, 92, 92, 191, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 714 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045115 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045115 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045115/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045115 Building REAL250005045116 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045116' /scratch/stefan/7916127/working/building/REAL250005045116 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045116 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045116/0 /scratch/stefan/7916127/working/building/REAL250005045116 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/233 `/scratch/stefan/7916127/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045116.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045116 none CCC1CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.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', '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, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 194, 194, 165, 66, 66, 66, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 201, 201, 201, 201, 201, 194, 194, 194, 165, 165, 66, 25, 25, 14, 14, 4, 1, 194, 194] 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: REAL250005045116 none CCC1CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.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', '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, 10, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 6, 25, 25, 25, 88, 106, 186, 186, 186, 194, 194, 194, 194, 194, 1, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 25, 88, 88, 106, 106, 186, 194, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 38, 39, 20, 26, 27, 28] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045116 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045116/1 /scratch/stefan/7916127/working/building/REAL250005045116 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/234 `/scratch/stefan/7916127/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1C[NH+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045116.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045116 none CCC1C[NH+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 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, 57, 57, 57, 49, 57, 26, 26, 26, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 57, 62, 62, 62, 62, 62, 57, 57, 57, 49, 49, 26, 14, 14, 14, 14, 5, 1, 57, 57] 62 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, 39, 40]) total number of confs: 255 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045116 none CCC1C[NH+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 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: [3, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 41, 41, 42, 42, 42, 57, 57, 57, 57, 57, 1, 3, 3, 3, 3, 3, 1, 1, 1, 6, 6, 22, 41, 41, 41, 41, 42, 57, 1, 1] 62 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 21, 27, 28, 29] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045116 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045116 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045116/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045116/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045116 Building REAL250005045117 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045117' /scratch/stefan/7916127/working/building/REAL250005045117 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045117 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045117/0 /scratch/stefan/7916127/working/building/REAL250005045117 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/235 `/scratch/stefan/7916127/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045117.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045117 none CC1=CN(C)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 162, 106, 106, 106, 43, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 162, 106, 43, 43, 26, 26, 9, 1] 162 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: 438 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045117 none CC1=CN(C)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 64, 93, 154, 154, 154, 162, 162, 162, 162, 162, 2, 2, 2, 1, 2, 2, 2, 1, 12, 63, 63, 93, 93, 154, 162] 162 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 603 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045117 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045117 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045117/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045117 Building REAL250005045118 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045118' /scratch/stefan/7916127/working/building/REAL250005045118 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045118 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045118/0 /scratch/stefan/7916127/working/building/REAL250005045118 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/236 `/scratch/stefan/7916127/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC=CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045118.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045118 none C=CC=CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 139, 55, 55, 55, 23, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 139, 139, 55, 23, 23, 16, 16, 4, 1] 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]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045118 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045118 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045118/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045118 Building REAL250005045119 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045119' /scratch/stefan/7916127/working/building/REAL250005045119 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045119 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045119/0 /scratch/stefan/7916127/working/building/REAL250005045119 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/237 `/scratch/stefan/7916127/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045119.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045119 none C#CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', '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, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 103, 103, 45, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 103, 45, 45, 28, 28, 6, 1, 201, 201, 201, 201, 201, 201] 201 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, 33]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045119 none C#CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', '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, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 49, 89, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 49, 49, 89, 89, 201, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 32, 17, 18, 19, 20, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045119 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045119 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045119/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045119 Building REAL250005045120 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045120' /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045120 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045120/0 /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/238 `/scratch/stefan/7916127/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045120.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045120 none C[N@@H+]1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 8, 1] 23 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: 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: REAL250005045120 none C[N@@H+]1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 15, 16, 16, 16, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 11, 11, 15, 15, 16, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045120/1 /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/239 `/scratch/stefan/7916127/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045120.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045120 none C[N@H+]1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 7, 1] 9 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: 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: REAL250005045120 none C[N@H+]1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 6, 6, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 6, 6, 6, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045120/2 /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/240 `/scratch/stefan/7916127/working/3D/240' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045120.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045120/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045120 none CN1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 98, 119, 98, 99, 47, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 119, 119, 99, 47, 47, 32, 32, 8, 1] 119 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: 397 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045120 none CN1CCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 68, 114, 114, 114, 119, 119, 119, 119, 119, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 40, 40, 68, 68, 114, 119] 119 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 444 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045120 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045120 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045120/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045120/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045120/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045120 Building REAL250005045121 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045121' /scratch/stefan/7916127/working/building/REAL250005045121 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045121 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045121/0 /scratch/stefan/7916127/working/building/REAL250005045121 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/241 `/scratch/stefan/7916127/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC=CC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045121.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045121 none CCCC=CC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 5, 12, 1, 11, 8, 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, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 176, 127, 127, 86, 40, 86, 40, 40, 15, 10, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 176, 176, 127, 127, 86, 258, 40, 15, 15, 10, 10, 3, 1] 603 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: 1185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045121 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045121 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045121/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045121 Building REAL250005045122 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045122' /scratch/stefan/7916127/working/building/REAL250005045122 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045122 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045122/0 /scratch/stefan/7916127/working/building/REAL250005045122 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/242 `/scratch/stefan/7916127/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC=CCO1)C1=CC(=O)[N-]O1) `REAL250005045122.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045122 none O=C(NCCNC(=O)C1CC=CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 25, 34, 81, 81, 81, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 7, 25, 25, 34, 34, 81, 129, 129, 129, 129, 129, 129, 129, 1] 129 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 408 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: REAL250005045122 none O=C(NCCNC(=O)C1CC=CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 1, 1, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 78, 62, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 128, 129, 129, 129, 129, 129, 128, 78, 78, 62, 62, 13, 1, 1, 1, 1, 1, 1, 1, 129] 129 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 471 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045122 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045122 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045122/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045122 Building REAL250005045123 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045123' /scratch/stefan/7916127/working/building/REAL250005045123 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045123 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045123/0 /scratch/stefan/7916127/working/building/REAL250005045123 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/243 `/scratch/stefan/7916127/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CCCO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045123.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045123 none CC(C)(CCCO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', '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', 'H', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 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, 7, 4, 7, 6, 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, 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: [140, 71, 140, 138, 193, 201, 201, 71, 71, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 141, 141, 140, 141, 140, 141, 201, 201, 201, 201, 201, 201, 603, 71, 23, 23, 14, 14, 4, 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: 1568 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045123 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045123 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045123/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045123 Building REAL250005045124 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045124' /scratch/stefan/7916127/working/building/REAL250005045124 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045124 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045124/0 /scratch/stefan/7916127/working/building/REAL250005045124 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/244 `/scratch/stefan/7916127/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045124.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045124 none O=C(CCOC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 100, 123, 173, 201, 201, 22, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 100, 100, 123, 123, 201, 201, 201, 201, 201, 32, 22, 22, 14, 14, 4, 1] 201 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: 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: REAL250005045124 none O=C(CCOC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 42, 23, 7, 1, 1, 1, 1, 110, 110, 176, 185, 201, 201, 201, 201, 201, 201, 201, 201, 42, 42, 23, 23, 1, 1, 1, 1, 1, 110, 176, 176, 185, 185, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045124 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045124 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045124/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045124 Building REAL250005045125 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045125' /scratch/stefan/7916127/working/building/REAL250005045125 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045125 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045125/0 /scratch/stefan/7916127/working/building/REAL250005045125 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/245 `/scratch/stefan/7916127/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCCCO)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045125.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045125 none O=C(CCCCCO)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 8, 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: [6, 7, 7, 7, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 167, 173, 195, 189, 201, 32, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 168, 168, 186, 186, 195, 195, 201, 201, 196, 197, 603, 44, 32, 32, 17, 17, 4, 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: 1604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045125 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045125 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045125/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045125 Building REAL250005045126 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045126' /scratch/stefan/7916127/working/building/REAL250005045126 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045126 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045126/0 /scratch/stefan/7916127/working/building/REAL250005045126 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/246 `/scratch/stefan/7916127/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=N1) `REAL250005045126.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045126 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [4, 1, 4, 4, 23, 35, 67, 67, 67, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 4, 22, 22, 36, 36, 67, 73, 1, 1] 73 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) 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: REAL250005045126 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [71, 71, 41, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 73, 73, 73, 73, 71, 41, 41, 28, 28, 9, 1, 73, 73] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045126 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045126 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045126/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045126 Building REAL250005045127 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045127' /scratch/stefan/7916127/working/building/REAL250005045127 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045127 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045127/0 /scratch/stefan/7916127/working/building/REAL250005045127 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/247 `/scratch/stefan/7916127/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[NH+]1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045127.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045127 none O=C(C[NH+]1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 9, 6, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 1, 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, 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: [33, 33, 33, 41, 45, 45, 45, 45, 45, 45, 16, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 41, 41, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 33, 16, 16, 12, 12, 4, 1] 45 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: 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: REAL250005045127 none O=C(C[NH+]1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 9, 6, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 1, 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, 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: [15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 27, 35, 45, 45, 45, 45, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 27, 27, 35, 35, 45, 45] 45 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 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/7916127/working/building/REAL250005045127 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045127/1 /scratch/stefan/7916127/working/building/REAL250005045127 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/248 `/scratch/stefan/7916127/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045127.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045127/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045127 none O=C(CN1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 197, 201, 201, 201, 201, 201, 38, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 120, 38, 38, 23, 23, 4, 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: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045127 none O=C(CN1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 6, 1, 1, 1, 1, 1, 1, 1, 17, 17, 65, 103, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 65, 65, 103, 103, 201, 201] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 732 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045127 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045127 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045127/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045127/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045127 Building REAL250005045128 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045128' /scratch/stefan/7916127/working/building/REAL250005045128 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045128 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045128/0 /scratch/stefan/7916127/working/building/REAL250005045128 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/249 `/scratch/stefan/7916127/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CO)CCC1)C1=CC(=O)[N-]O1) `REAL250005045128.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045128 none O=C(NCCNC(=O)C1(CO)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [4, 1, 4, 3, 23, 36, 87, 87, 87, 175, 201, 175, 175, 175, 1, 1, 1, 1, 1, 1, 4, 23, 23, 36, 36, 87, 201, 201, 603, 175, 175, 175, 175, 175, 175, 1] 603 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1328 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045128 none O=C(NCCNC(=O)C1(CO)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [167, 163, 62, 39, 6, 6, 1, 6, 1, 1, 7, 1, 1, 1, 167, 175, 175, 175, 175, 175, 167, 62, 62, 39, 39, 6, 7, 7, 21, 1, 1, 1, 1, 1, 1, 175] 603 rigid atoms, others: [32, 33, 34, 6, 8, 9, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 638 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045128 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045128 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045128/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045128 Building REAL250005045129 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045129' /scratch/stefan/7916127/working/building/REAL250005045129 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045129 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045129/0 /scratch/stefan/7916127/working/building/REAL250005045129 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/250 `/scratch/stefan/7916127/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCCC1O)C1=CC(=O)[N-]O1) `REAL250005045129.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045129 none O=C(NCCNC(=O)C1CCCCC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 39, 54, 124, 124, 124, 181, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 11, 39, 39, 54, 54, 124, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 543, 1] 543 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: 1153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045129 none O=C(NCCNC(=O)C1CCCCC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [173, 171, 94, 57, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 171, 181, 181, 181, 181, 181, 173, 94, 94, 57, 57, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 181] 543 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045129 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045129 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045129/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045129 Building REAL250005045130 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045130' /scratch/stefan/7916127/working/building/REAL250005045130 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045130 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045130/0 /scratch/stefan/7916127/working/building/REAL250005045130 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/251 `/scratch/stefan/7916127/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CN=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045130.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045130 none CN1C=CN=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 88, 88, 88, 37, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 88, 37, 37, 23, 23, 6, 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: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045130 none CN1C=CN=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 27, 81, 110, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 7, 7, 27, 81, 81, 110, 110, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([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]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045130 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045130 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045130/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045130 Building REAL250005045131 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045131' /scratch/stefan/7916127/working/building/REAL250005045131 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045131 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045131/0 /scratch/stefan/7916127/working/building/REAL250005045131 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/252 `/scratch/stefan/7916127/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C) `REAL250005045131.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045131 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 4, 1, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 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: REAL250005045131 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 10, 11, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 7, 7, 10, 10, 11, 14, 1, 1, 1, 1, 2, 2, 2] 14 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 34, 17, 18, 19, 20, 21, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045131 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045131/1 /scratch/stefan/7916127/working/building/REAL250005045131 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/253 `/scratch/stefan/7916127/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C) `REAL250005045131.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045131 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 37, 20, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 37, 20, 20, 19, 19, 8, 1, 42, 42, 42, 42, 42, 42, 42] 42 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 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: REAL250005045131 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 22, 26, 28, 28, 28, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 22, 22, 26, 26, 28, 42, 1, 1, 1, 1, 2, 2, 2] 42 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 34, 17, 18, 19, 20, 21, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045131 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045131 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045131/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045131/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045131 Building REAL250005045132 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045132' /scratch/stefan/7916127/working/building/REAL250005045132 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045132 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045132/0 /scratch/stefan/7916127/working/building/REAL250005045132 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/254 `/scratch/stefan/7916127/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045132.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045132 none O=C(NCCNC(=O)C1=CN=CC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 37, 91, 91, 91, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 9, 28, 28, 37, 37, 91, 147, 147, 147, 1] 147 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 372 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: REAL250005045132 none O=C(NCCNC(=O)C1=CN=CC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 83, 54, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 143, 147, 147, 147, 147, 147, 143, 83, 83, 54, 54, 10, 1, 1, 1, 147] 147 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 547 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045132 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045132 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045132/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045132 Building REAL250005045133 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045133' /scratch/stefan/7916127/working/building/REAL250005045133 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045133 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045133/0 /scratch/stefan/7916127/working/building/REAL250005045133 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/255 `/scratch/stefan/7916127/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CNC(=O)S1)C1=CC(=O)[N-]O1) `REAL250005045133.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045133 none O=C(NCCNC(=O)C1=CNC(=O)S1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 30, 39, 89, 89, 89, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 9, 30, 30, 39, 39, 89, 118, 118, 1] 118 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045133 none O=C(NCCNC(=O)C1=CNC(=O)S1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 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: [112, 112, 63, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 112, 118, 118, 118, 118, 118, 112, 64, 64, 48, 48, 13, 1, 1, 118] 118 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045133 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045133 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045133/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045133 Building REAL250005045134 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045134' /scratch/stefan/7916127/working/building/REAL250005045134 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045134 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045134/0 /scratch/stefan/7916127/working/building/REAL250005045134 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/256 `/scratch/stefan/7916127/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045134.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045134 none NC(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 153, 90, 90, 90, 31, 20, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 171, 171, 153, 153, 90, 31, 31, 20, 20, 6, 1] 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]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045134 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045134 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045134/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045134 Building REAL250005045135 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045135' /scratch/stefan/7916127/working/building/REAL250005045135 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045135 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045135/0 /scratch/stefan/7916127/working/building/REAL250005045135 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/257 `/scratch/stefan/7916127/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045135.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045135 none C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 171, 78, 78, 78, 32, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 78, 32, 32, 19, 19, 4, 1, 171, 171, 171, 171] 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: 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: REAL250005045135 none C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 7, 7, 7, 42, 59, 157, 157, 157, 171, 171, 171, 171, 171, 1, 1, 17, 17, 17, 5, 5, 7, 42, 42, 59, 59, 157, 171, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 18, 19] set([0, 1, 5, 6, 7, 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: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045135 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045135 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045135/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045135 Building REAL250005045136 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045136' /scratch/stefan/7916127/working/building/REAL250005045136 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045136 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045136/0 /scratch/stefan/7916127/working/building/REAL250005045136 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/258 `/scratch/stefan/7916127/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045136.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045136 none O=C(COC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens 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, 142, 194, 201, 201, 21, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 142, 142, 201, 61, 21, 21, 12, 12, 4, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045136 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045136 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045136/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045136 Building REAL250005045137 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045137' /scratch/stefan/7916127/working/building/REAL250005045137 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045137 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045137/0 /scratch/stefan/7916127/working/building/REAL250005045137 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/259 `/scratch/stefan/7916127/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1) `REAL250005045137.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045137 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1 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.2', 'O.2', 'N.am', '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, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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, 129, 129, 129, 52, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 183, 183, 129, 52, 52, 36, 36, 11, 1, 183, 183, 183, 183, 183] 183 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045137 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1 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.2', 'O.2', 'N.am', '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, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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: [1, 1, 1, 11, 11, 11, 50, 85, 169, 170, 169, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 2, 2, 2, 11, 50, 50, 85, 85, 170, 183, 1, 1, 1, 1, 1] 183 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045137 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045137 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045137/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045137 Building REAL250005045138 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045138' /scratch/stefan/7916127/working/building/REAL250005045138 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045138 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045138/0 /scratch/stefan/7916127/working/building/REAL250005045138 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/260 `/scratch/stefan/7916127/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045138.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045138 none COC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 112, 191, 191, 54, 54, 54, 24, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 192, 192, 192, 192, 192, 192, 112, 112, 54, 24, 24, 17, 17, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045138 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045138 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045138/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045138 Building REAL250005045139 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045139' /scratch/stefan/7916127/working/building/REAL250005045139 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045139 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045139/0 /scratch/stefan/7916127/working/building/REAL250005045139 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/261 `/scratch/stefan/7916127/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045139.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045139 none CC(O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [200, 148, 201, 142, 74, 74, 74, 35, 23, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 200, 197, 603, 169, 169, 142, 142, 74, 35, 35, 23, 23, 7, 1] 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]) total number of confs: 1576 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045139 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045139 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045139/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045139 Building REAL250005045140 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045140' /scratch/stefan/7916127/working/building/REAL250005045140 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045140 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045140/0 /scratch/stefan/7916127/working/building/REAL250005045140 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/262 `/scratch/stefan/7916127/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(O)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045140.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 Warning: Using closest atom type 60 for atom 3 Warning: Using closest atom type 60 for atom 3 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045140 none CCS(O)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 168, 168, 104, 104, 104, 37, 24, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 104, 37, 37, 24, 24, 8, 1] 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]) total number of confs: 727 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045140 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045140 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045140/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045140 Building REAL250005045141 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045141' /scratch/stefan/7916127/working/building/REAL250005045141 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045141 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045141/0 /scratch/stefan/7916127/working/building/REAL250005045141 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/263 `/scratch/stefan/7916127/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045141.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045141 none CN(C)C(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 6, 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] 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, 5, 5, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 4, 1] 9 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: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045141 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045141 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045141/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045141 Building REAL250005045142 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045142' /scratch/stefan/7916127/working/building/REAL250005045142 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045142 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045142/0 /scratch/stefan/7916127/working/building/REAL250005045142 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/264 `/scratch/stefan/7916127/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045142.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045142 none C#CCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 82, 156, 82, 82, 33, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 156, 156, 156, 156, 82, 33, 33, 21, 21, 4, 1] 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]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045142 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045142 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045142/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045142 Building REAL250005045143 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045143' /scratch/stefan/7916127/working/building/REAL250005045143 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045143 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045143/0 /scratch/stefan/7916127/working/building/REAL250005045143 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/265 `/scratch/stefan/7916127/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CCO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045143.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045143 none CC(CCO)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 378 conformations in input total number of sets (complete confs): 378 using faster count positions algorithm for large data unique positions, atoms: [104, 45, 104, 124, 126, 45, 45, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 124, 124, 126, 126, 378, 45, 23, 23, 14, 14, 4, 1] 378 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: 935 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045143 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045143 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045143/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045143 Building REAL250005045144 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045144' /scratch/stefan/7916127/working/building/REAL250005045144 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045144 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045144/0 /scratch/stefan/7916127/working/building/REAL250005045144 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/266 `/scratch/stefan/7916127/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=CC1CC1) `REAL250005045144.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045144 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 8, 45, 45, 114, 145, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 45, 114, 114, 145, 145, 201, 201, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 765 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: REAL250005045144 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=CC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 39, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 105, 147, 147, 147, 201, 201, 105, 39, 39, 25, 25, 4, 1, 147, 201, 201, 201, 201, 201] 201 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: 682 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045144 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045144 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045144/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045144 Building REAL250005045145 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045145' /scratch/stefan/7916127/working/building/REAL250005045145 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045145 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045145/0 /scratch/stefan/7916127/working/building/REAL250005045145 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/267 `/scratch/stefan/7916127/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC(F)C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045145.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045145 none O=C(CC1CC(F)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 15, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 158, 201, 201, 201, 201, 31, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 158, 158, 201, 201, 201, 201, 201, 201, 65, 31, 31, 20, 20, 4, 1] 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]) total number of confs: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045145 none O=C(CC1CC(F)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 15, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 6, 1, 1, 1, 1, 1, 1, 34, 34, 120, 143, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 34, 120, 120, 143, 143, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045145 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045145 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045145/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045145 Building REAL250005045146 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045146' /scratch/stefan/7916127/working/building/REAL250005045146 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045146 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045146/0 /scratch/stefan/7916127/working/building/REAL250005045146 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/268 `/scratch/stefan/7916127/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C(F)CC1CCC1)C1=CC(=O)[N-]O1) `REAL250005045146.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045146 none O=C(NCCNC(=O)C(F)CC1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 2, 9, 15, 40, 40, 40, 99, 99, 152, 201, 201, 201, 1, 1, 1, 1, 1, 1, 2, 9, 9, 15, 15, 40, 99, 152, 152, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 37, 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]) total number of confs: 862 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045146 none O=C(NCCNC(=O)C(F)CC1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 158, 145, 66, 66, 14, 66, 5, 14, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 157, 158, 146, 146, 66, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045146 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045146 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045146/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045146 Building REAL250005045147 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045147' /scratch/stefan/7916127/working/building/REAL250005045147 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045147 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045147/0 /scratch/stefan/7916127/working/building/REAL250005045147 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/269 `/scratch/stefan/7916127/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H](O)CF)C1=CC(=O)[N-]O1) `REAL250005045147.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045147 none O=C(NCCNC(=O)[C@H](O)CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 12, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 24, 34, 88, 88, 88, 194, 194, 193, 201, 1, 1, 1, 1, 1, 1, 8, 24, 24, 34, 34, 88, 582, 201, 201, 1] 603 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 1366 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045147 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045147 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045147/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045147 Building REAL250005045148 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045148' /scratch/stefan/7916127/working/building/REAL250005045148 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045148 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045148/0 /scratch/stefan/7916127/working/building/REAL250005045148 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/270 `/scratch/stefan/7916127/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045148.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045148 none CCC1(C)C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 175, 175, 175, 175, 92, 92, 92, 35, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 175, 201, 201, 201, 201, 201, 175, 175, 175, 175, 92, 35, 35, 22, 22, 5, 1, 175, 175] 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, 37, 38]) total number of confs: 583 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: REAL250005045148 none CCC1(C)C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 55, 81, 163, 163, 163, 175, 175, 175, 175, 175, 1, 4, 4, 4, 3, 3, 2, 2, 2, 1, 13, 55, 55, 81, 81, 163, 175, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 38, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 613 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045148 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045148 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045148/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045148 Building REAL250005045149 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045149' /scratch/stefan/7916127/working/building/REAL250005045149 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045149 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045149/0 /scratch/stefan/7916127/working/building/REAL250005045149 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/271 `/scratch/stefan/7916127/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045149.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045149 none CCC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 187, 187, 187, 79, 79, 79, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 187, 187, 187, 187, 187, 187, 79, 30, 30, 19, 19, 4, 1, 187, 187] 201 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: 663 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: REAL250005045149 none CCC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 63, 83, 180, 180, 180, 187, 187, 187, 187, 187, 1, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 11, 63, 63, 83, 83, 180, 187, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 39, 40, 20, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 644 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045149 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045149 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045149/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045149 Building REAL250005045150 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045150' /scratch/stefan/7916127/working/building/REAL250005045150 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045150 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045150/0 /scratch/stefan/7916127/working/building/REAL250005045150 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/272 `/scratch/stefan/7916127/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045150.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045150 none CCN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 142, 142, 142, 142, 92, 92, 92, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 142, 92, 33, 33, 20, 20, 4, 1] 201 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]) total number of confs: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045150 none CCN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 6, 6, 6, 35, 57, 137, 137, 137, 142, 142, 142, 142, 142, 1, 9, 9, 9, 9, 9, 1, 6, 34, 34, 57, 57, 137, 142] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045150 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045150 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045150/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045150 Building REAL250005045151 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045151' /scratch/stefan/7916127/working/building/REAL250005045151 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045151 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045151/0 /scratch/stefan/7916127/working/building/REAL250005045151 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/273 `/scratch/stefan/7916127/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045151.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045151 none CCCC(C)(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 6, 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, 7, 7] 1 hydrogens need rotated 585 conformations in input total number of sets (complete confs): 585 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 173, 112, 174, 177, 50, 50, 50, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 195, 195, 195, 177, 177, 177, 531, 112, 112, 50, 19, 19, 12, 12, 4, 1] 585 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: 1437 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045151 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045151 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045151/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045151 Building REAL250005045152 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045152' /scratch/stefan/7916127/working/building/REAL250005045152 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045152 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045152/0 /scratch/stefan/7916127/working/building/REAL250005045152 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/274 `/scratch/stefan/7916127/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045152.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045152 none CN1C=NN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 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, 80, 78, 78, 78, 38, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 78, 38, 38, 25, 25, 7, 1] 80 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]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045152 none CN1C=NN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 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, 4, 4, 4, 20, 34, 76, 76, 76, 80, 80, 80, 80, 80, 2, 2, 2, 1, 4, 20, 20, 34, 34, 76, 80] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045152 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045152 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045152/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045152 Building REAL250005045153 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045153' /scratch/stefan/7916127/working/building/REAL250005045153 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045153 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045153/0 /scratch/stefan/7916127/working/building/REAL250005045153 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/275 `/scratch/stefan/7916127/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045153.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045153 none CCCC(CC)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 131, 88, 132, 177, 21, 21, 21, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 188, 188, 138, 177, 171, 177, 177, 177, 88, 88, 21, 19, 19, 12, 12, 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: 1146 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045153 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045153 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045153/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045153 Building REAL250005045154 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045154' /scratch/stefan/7916127/working/building/REAL250005045154 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045154 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045154/0 /scratch/stefan/7916127/working/building/REAL250005045154 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/276 `/scratch/stefan/7916127/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045154.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045154 none CC1=CON=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 181, 82, 82, 82, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 181, 181, 82, 33, 33, 20, 20, 4, 1] 201 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]) total number of confs: 729 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045154 none CC1=CON=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 31, 31, 31, 82, 120, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 8, 8, 31, 82, 82, 120, 120, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045154 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045154 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045154/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045154 Building REAL250005045155 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045155' /scratch/stefan/7916127/working/building/REAL250005045155 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045155 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045155/0 /scratch/stefan/7916127/working/building/REAL250005045155 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/277 `/scratch/stefan/7916127/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045155.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045155 none C#CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 103, 103, 103, 55, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 103, 55, 55, 34, 34, 9, 1, 201] 201 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, 33]) total number of confs: 532 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045155 none C#CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 37, 71, 189, 189, 189, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 5, 37, 37, 71, 71, 189, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 21, 22, 23, 24, 25, 33] set([32, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31]) total number of confs: 671 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045155 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045155 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045155/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045155 Building REAL250005045156 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045156' /scratch/stefan/7916127/working/building/REAL250005045156 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045156 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045156/0 /scratch/stefan/7916127/working/building/REAL250005045156 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/278 `/scratch/stefan/7916127/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(O)CCCCC1)C1=CC(=O)[N-]O1) `REAL250005045156.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045156 none O=C(NCCNC(=O)C1(O)CCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 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] 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: [9, 1, 9, 8, 27, 38, 103, 103, 103, 160, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 9, 27, 27, 38, 38, 103, 480, 160, 160, 160, 160, 160, 160, 160, 160, 160, 160, 1] 480 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: 1011 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045156 none O=C(NCCNC(=O)C1(O)CCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 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] 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: [154, 153, 91, 68, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 154, 160, 160, 160, 160, 160, 154, 91, 91, 68, 68, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 160] 480 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045156 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045156 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045156/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045156 Building REAL250005045157 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045157' /scratch/stefan/7916127/working/building/REAL250005045157 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045157 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045157/0 /scratch/stefan/7916127/working/building/REAL250005045157 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/279 `/scratch/stefan/7916127/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(O)CC1)C1=CC(=O)[N-]O1) `REAL250005045157.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045157 none O=C(NCCNC(=O)C1(O)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [9, 1, 9, 9, 32, 44, 98, 98, 98, 183, 183, 183, 1, 1, 1, 1, 1, 1, 9, 32, 32, 44, 44, 98, 549, 183, 183, 183, 183, 1] 549 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 1130 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045157 none O=C(NCCNC(=O)C1(O)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [174, 174, 105, 74, 12, 12, 1, 12, 1, 1, 1, 1, 174, 183, 183, 183, 183, 183, 174, 105, 105, 74, 74, 12, 6, 1, 1, 1, 1, 183] 549 rigid atoms, others: [6, 8, 9, 10, 11, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29]) total number of confs: 678 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045157 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045157 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045157/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045157 Building REAL250005045158 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045158' /scratch/stefan/7916127/working/building/REAL250005045158 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045158 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045158/0 /scratch/stefan/7916127/working/building/REAL250005045158 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/280 `/scratch/stefan/7916127/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NS(=O)(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045158.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045158 none NS(=O)(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'S.o2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 6, 7, 7, 6, 4, 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 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, 201, 103, 103, 103, 43, 30, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 173, 173, 103, 43, 43, 30, 30, 9, 1] 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]) total number of confs: 819 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045158 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045158 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045158/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045158 Building REAL250005045159 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045159' /scratch/stefan/7916127/working/building/REAL250005045159 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045159 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045159/0 /scratch/stefan/7916127/working/building/REAL250005045159 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/281 `/scratch/stefan/7916127/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NS1) `REAL250005045159.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045159 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NS1 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.2', 'N.2', 'S.3', '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, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 102, 102, 102, 44, 25, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 102, 44, 44, 25, 25, 8, 1, 184] 184 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]) 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: REAL250005045159 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NS1 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.2', 'N.2', 'S.3', '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, 1, 8, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 55, 99, 180, 182, 180, 184, 184, 184, 184, 184, 1, 1, 1, 2, 2, 2, 9, 55, 55, 99, 99, 182, 184, 1] 184 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045159 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045159 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045159/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045159 Building REAL250005045160 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045160' /scratch/stefan/7916127/working/building/REAL250005045160 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045160 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045160/0 /scratch/stefan/7916127/working/building/REAL250005045160 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/282 `/scratch/stefan/7916127/working/3D/282' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045160.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045160 none O=C(CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 168, 201, 201, 36, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 99, 36, 36, 23, 23, 5, 1] 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]) total number of confs: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045160 none O=C(CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 3, 1, 1, 1, 1, 25, 25, 107, 146, 201, 201, 201, 201, 201, 201, 201, 201, 3, 3, 1, 1, 1, 1, 1, 25, 107, 107, 146, 146, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 20, 21, 22, 23, 24] set([0, 1, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045160 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045160 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045160/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045160 Building REAL250005045161 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045161' /scratch/stefan/7916127/working/building/REAL250005045161 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045161 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045161/0 /scratch/stefan/7916127/working/building/REAL250005045161 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/283 `/scratch/stefan/7916127/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045161.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045161 none CC(C)(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 123, 179, 179, 123, 123, 56, 35, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 179, 179, 179, 179, 179, 179, 123, 56, 56, 35, 35, 9, 1] 179 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]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045161 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045161 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045161/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045161 Building REAL250005045162 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045162' /scratch/stefan/7916127/working/building/REAL250005045162 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045162 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045162/0 /scratch/stefan/7916127/working/building/REAL250005045162 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/284 `/scratch/stefan/7916127/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045162.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045162 none CC(F)(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 114, 201, 201, 114, 114, 49, 34, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 114, 49, 49, 34, 34, 11, 1] 201 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]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045162 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045162 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045162/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045162 Building REAL250005045163 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045163' /scratch/stefan/7916127/working/building/REAL250005045163 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045163 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045163/0 /scratch/stefan/7916127/working/building/REAL250005045163 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/285 `/scratch/stefan/7916127/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC=N1)C1=CC(=O)[N-]O1) `REAL250005045163.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045163 none O=C(NCCNC(=O)C1=CC=CC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [4, 1, 4, 4, 14, 19, 39, 39, 39, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 4, 14, 14, 19, 19, 39, 61, 61, 61, 61, 1] 61 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 164 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045163 none O=C(NCCNC(=O)C1=CC=CC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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, 45, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 45, 45, 35, 35, 11, 1, 1, 1, 1, 61] 61 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045163 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045163 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045163/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045163 Building REAL250005045164 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045164' /scratch/stefan/7916127/working/building/REAL250005045164 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045164 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045164/0 /scratch/stefan/7916127/working/building/REAL250005045164 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/286 `/scratch/stefan/7916127/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=NC=C1)C1=CC(=O)[N-]O1) `REAL250005045164.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045164 none O=C(NCCNC(=O)C1=CC=NC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 32, 43, 73, 73, 73, 75, 75, 73, 75, 75, 1, 1, 1, 1, 1, 1, 11, 32, 32, 43, 43, 73, 75, 75, 75, 75, 1] 75 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005045164 none O=C(NCCNC(=O)C1=CC=NC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 35, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 69, 75, 75, 75, 75, 75, 69, 35, 35, 16, 16, 4, 1, 1, 1, 1, 75] 75 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 263 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045164 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045164 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045164/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045164 Building REAL250005045165 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045165' /scratch/stefan/7916127/working/building/REAL250005045165 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045165 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045165/0 /scratch/stefan/7916127/working/building/REAL250005045165 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/287 `/scratch/stefan/7916127/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=C(F)C=C1)C1=CC(=O)[N-]O1) `REAL250005045165.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045165 none O=C(NCCNC(=O)C1=CC=C(F)C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 32, 45, 77, 77, 77, 79, 79, 78, 79, 79, 79, 1, 1, 1, 1, 1, 1, 11, 32, 32, 45, 45, 77, 79, 79, 79, 79, 1] 79 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) 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: REAL250005045165 none O=C(NCCNC(=O)C1=CC=C(F)C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 37, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 71, 79, 79, 79, 79, 79, 71, 37, 37, 16, 16, 4, 1, 1, 1, 1, 79] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 273 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045165 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045165 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045165/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045165 Building REAL250005045166 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045166' /scratch/stefan/7916127/working/building/REAL250005045166 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045166 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045166/0 /scratch/stefan/7916127/working/building/REAL250005045166 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/288 `/scratch/stefan/7916127/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CN=C1)C1=CC(=O)[N-]O1) `REAL250005045166.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045166 none O=C(NCCNC(=O)C1=CC=CN=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 34, 49, 93, 93, 93, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 11, 34, 34, 49, 49, 93, 117, 117, 117, 117, 1] 117 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045166 none O=C(NCCNC(=O)C1=CC=CN=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [111, 111, 57, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 111, 117, 117, 117, 117, 117, 111, 57, 57, 31, 31, 7, 1, 1, 1, 1, 117] 117 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045166 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045166 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045166/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045166 Building REAL250005045167 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045167' /scratch/stefan/7916127/working/building/REAL250005045167 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045167 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045167/0 /scratch/stefan/7916127/working/building/REAL250005045167 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/289 `/scratch/stefan/7916127/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CS1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045167.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045167 none O=C(CC1=CC=CS1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 127, 201, 201, 201, 201, 19, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 49, 19, 19, 14, 14, 4, 1] 201 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]) total number of confs: 621 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045167 none O=C(CC1=CC=CS1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 27, 27, 117, 135, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 27, 117, 117, 135, 135, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045167 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045167 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045167/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045167 Building REAL250005045168 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045168' /scratch/stefan/7916127/working/building/REAL250005045168 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045168 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045168/0 /scratch/stefan/7916127/working/building/REAL250005045168 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/290 `/scratch/stefan/7916127/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CO1) `REAL250005045168.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045168 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 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: [6, 1, 6, 6, 24, 39, 74, 74, 74, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 6, 23, 23, 39, 39, 74, 81, 1, 1, 1] 81 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) 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: REAL250005045168 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 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: [72, 72, 41, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 72, 81, 81, 81, 81, 72, 41, 41, 29, 29, 8, 1, 81, 81, 81] 81 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 272 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045168 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045168 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045168/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045168 Building REAL250005045169 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045169' /scratch/stefan/7916127/working/building/REAL250005045169 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045169 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045169/0 /scratch/stefan/7916127/working/building/REAL250005045169 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/291 `/scratch/stefan/7916127/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045169.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045169 none CC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 193, 108, 108, 108, 38, 23, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 193, 193, 108, 38, 38, 23, 23, 4, 1] 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]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045169 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045169 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045169/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045169 Building REAL250005045170 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045170' /scratch/stefan/7916127/working/building/REAL250005045170 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045170 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045170/0 /scratch/stefan/7916127/working/building/REAL250005045170 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/292 `/scratch/stefan/7916127/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SC=C1) `REAL250005045170.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045170 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SC=C1 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', 'S.3', 'C.2', 'C.2', '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, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 50, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 128, 50, 50, 30, 30, 9, 1, 201, 201] 201 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]) total number of confs: 540 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045170 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SC=C1 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', 'S.3', 'C.2', 'C.2', '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, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 57, 102, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 57, 57, 102, 102, 195, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045170 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045170 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045170/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045170 Building REAL250005045171 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045171' /scratch/stefan/7916127/working/building/REAL250005045171 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045171 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045171/0 /scratch/stefan/7916127/working/building/REAL250005045171 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/293 `/scratch/stefan/7916127/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1) `REAL250005045171.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045171 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 117, 117, 117, 93, 93, 93, 42, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 93, 42, 42, 28, 28, 9, 1] 117 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]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045171 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 14, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 41, 62, 109, 109, 109, 117, 117, 117, 117, 117, 1, 2, 2, 2, 1, 1, 9, 41, 41, 62, 62, 109, 117] 117 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045171 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045171 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045171/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045171 Building REAL250005045172 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045172' /scratch/stefan/7916127/working/building/REAL250005045172 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045172 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045172/0 /scratch/stefan/7916127/working/building/REAL250005045172 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/294 `/scratch/stefan/7916127/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045172.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045172 none O=C(C=CC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 174, 174, 201, 201, 201, 201, 52, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 174, 174, 201, 201, 201, 105, 52, 52, 34, 34, 9, 1] 201 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: 609 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045172 none O=C(C=CC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 11, 11, 1, 1, 1, 1, 1, 1, 46, 45, 111, 136, 193, 193, 193, 201, 201, 201, 201, 201, 11, 11, 1, 1, 1, 46, 110, 110, 136, 136, 193, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045172 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045172 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045172/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045172 Building REAL250005045173 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045173' /scratch/stefan/7916127/working/building/REAL250005045173 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045173 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045173/0 /scratch/stefan/7916127/working/building/REAL250005045173 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/295 `/scratch/stefan/7916127/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC=C1F)C1=CC(=O)[N-]O1) `REAL250005045173.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045173 none O=C(NCCNC(=O)C1=CC=CC=C1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 47, 112, 112, 112, 191, 191, 142, 191, 191, 191, 1, 1, 1, 1, 1, 1, 9, 31, 31, 47, 47, 112, 191, 191, 191, 191, 1] 191 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 696 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045173 none O=C(NCCNC(=O)C1=CC=CC=C1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 115, 73, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 185, 191, 191, 191, 191, 191, 185, 115, 115, 73, 73, 13, 1, 1, 1, 1, 191] 191 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045173 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045173 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045173/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045173 Building REAL250005045174 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045174' /scratch/stefan/7916127/working/building/REAL250005045174 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045174 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045174/0 /scratch/stefan/7916127/working/building/REAL250005045174 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/296 `/scratch/stefan/7916127/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC=C1)C1=CC(=O)[N-]O1) `REAL250005045174.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045174 none O=C(NCCNC(=O)C1=CC=CC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 49, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 11, 34, 34, 49, 49, 75, 75, 75, 75, 75, 75, 1] 75 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045174 none O=C(NCCNC(=O)C1=CC=CC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 33, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 65, 75, 75, 75, 75, 75, 65, 33, 33, 15, 15, 3, 1, 1, 1, 1, 1, 75] 75 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 259 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045174 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045174 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045174/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045174 Building REAL250005045175 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045175' /scratch/stefan/7916127/working/building/REAL250005045175 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045175 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045175/0 /scratch/stefan/7916127/working/building/REAL250005045175 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/297 `/scratch/stefan/7916127/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045175.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045175 none CC(C)CC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 199, 201, 124, 124, 124, 51, 33, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 200, 201, 201, 201, 200, 200, 124, 51, 51, 33, 33, 10, 1] 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]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045175 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045175 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045175/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045175 Building REAL250005045176 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045176' /scratch/stefan/7916127/working/building/REAL250005045176 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045176 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045176/0 /scratch/stefan/7916127/working/building/REAL250005045176 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/298 `/scratch/stefan/7916127/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCCC1)C1=CC(=O)[N-]O1) `REAL250005045176.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045176 none O=C(NCCNC(=O)C1CCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [7, 1, 7, 7, 33, 50, 126, 126, 126, 200, 200, 201, 200, 200, 1, 1, 1, 1, 1, 1, 7, 33, 33, 50, 50, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 37, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 672 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045176 none O=C(NCCNC(=O)C1CCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [193, 191, 112, 64, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 192, 201, 201, 201, 201, 201, 193, 112, 112, 64, 64, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 37]) total number of confs: 761 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045176 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045176 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045176/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045176 Building REAL250005045177 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045177' /scratch/stefan/7916127/working/building/REAL250005045177 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045177 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045177/0 /scratch/stefan/7916127/working/building/REAL250005045177 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/299 `/scratch/stefan/7916127/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CC=N1)C1=CC(=O)[N-]O1) `REAL250005045177.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045177 none O=C(NCCNC(=O)C1=CN=CC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 14, 19, 35, 35, 35, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 5, 14, 14, 19, 19, 35, 45, 45, 45, 1] 45 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL250005045177 none O=C(NCCNC(=O)C1=CN=CC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [43, 43, 33, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 43, 45, 45, 45, 45, 45, 43, 33, 33, 24, 24, 8, 1, 1, 1, 45] 45 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045177 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045177 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045177/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045177 Building REAL250005045178 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045178' /scratch/stefan/7916127/working/building/REAL250005045178 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045178 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045178/0 /scratch/stefan/7916127/working/building/REAL250005045178 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/300 `/scratch/stefan/7916127/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045178.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045178 none CC1=CC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 124, 124, 124, 48, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 48, 48, 31, 31, 11, 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: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045178 none CC1=CC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 61, 103, 193, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 9, 61, 61, 103, 103, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045178 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045178 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045178/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045178 Building REAL250005045179 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045179' /scratch/stefan/7916127/working/building/REAL250005045179 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045179 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045179/0 /scratch/stefan/7916127/working/building/REAL250005045179 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/301 `/scratch/stefan/7916127/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045179.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045179 none O=C(CC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 176, 201, 201, 201, 201, 31, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 176, 176, 201, 201, 201, 201, 201, 201, 201, 201, 201, 58, 31, 31, 20, 20, 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: 769 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: REAL250005045179 none O=C(CC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 32, 32, 123, 144, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 123, 123, 144, 144, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 740 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045179 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045179 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045179/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045179 Building REAL250005045180 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045180' /scratch/stefan/7916127/working/building/REAL250005045180 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045180 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045180/0 /scratch/stefan/7916127/working/building/REAL250005045180 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/302 `/scratch/stefan/7916127/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045180.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045180 none O=C(CCC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 140, 141, 201, 201, 201, 201, 25, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 140, 140, 170, 170, 201, 201, 201, 201, 201, 201, 201, 201, 201, 43, 25, 25, 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: 956 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045180 none O=C(CCC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 1, 1, 1, 1, 1, 1, 40, 40, 127, 154, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 127, 127, 154, 154, 201, 201] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 815 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045180 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045180 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045180/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045180 Building REAL250005045181 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045181' /scratch/stefan/7916127/working/building/REAL250005045181 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045181 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045181/0 /scratch/stefan/7916127/working/building/REAL250005045181 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/303 `/scratch/stefan/7916127/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC(F)=C1)C1=CC(=O)[N-]O1) `REAL250005045181.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045181 none O=C(NCCNC(=O)C1=CC=CC(F)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 50, 89, 89, 89, 159, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 11, 34, 34, 50, 50, 89, 159, 159, 159, 159, 1] 159 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 423 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045181 none O=C(NCCNC(=O)C1=CC=CC(F)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [149, 149, 65, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 149, 159, 159, 159, 159, 159, 149, 65, 65, 35, 35, 7, 1, 1, 1, 1, 159] 159 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045181 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045181 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045181/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045181 Building REAL250005045182 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045182' /scratch/stefan/7916127/working/building/REAL250005045182 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045182 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045182/0 /scratch/stefan/7916127/working/building/REAL250005045182 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/304 `/scratch/stefan/7916127/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CS1)C1=CC(=O)[N-]O1) `REAL250005045182.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045182 none O=C(NCCNC(=O)C1=CC=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [7, 1, 7, 7, 28, 43, 89, 89, 89, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 7, 28, 28, 43, 43, 89, 127, 127, 127, 1] 127 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 380 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045182 none O=C(NCCNC(=O)C1=CC=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [121, 121, 75, 53, 11, 11, 1, 11, 1, 1, 1, 1, 1, 121, 127, 127, 127, 127, 127, 121, 75, 75, 53, 53, 11, 1, 1, 1, 127] 127 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045182 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045182 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045182/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045182 Building REAL250005045183 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045183' /scratch/stefan/7916127/working/building/REAL250005045183 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045183 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045183/0 /scratch/stefan/7916127/working/building/REAL250005045183 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/305 `/scratch/stefan/7916127/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1) `REAL250005045183.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045183 none CC1=CN=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 68, 68, 68, 68, 34, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 34, 34, 20, 20, 7, 1, 68] 68 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]) 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: REAL250005045183 none CC1=CN=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 20, 37, 64, 64, 64, 68, 68, 68, 68, 68, 1, 1, 2, 2, 2, 1, 3, 20, 20, 37, 37, 64, 68, 1] 68 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045183 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045183 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045183/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045183 Building REAL250005045184 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045184' /scratch/stefan/7916127/working/building/REAL250005045184 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045184 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045184/0 /scratch/stefan/7916127/working/building/REAL250005045184 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/306 `/scratch/stefan/7916127/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045184.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045184 none O=C(CC1=CSC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 114, 201, 201, 201, 201, 25, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 56, 25, 25, 16, 16, 4, 1] 201 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]) total number of confs: 638 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045184 none O=C(CC1=CSC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 4, 1, 1, 1, 1, 1, 1, 13, 13, 61, 86, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 13, 61, 61, 86, 86, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045184 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045184 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045184/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045184 Building REAL250005045185 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045185' /scratch/stefan/7916127/working/building/REAL250005045185 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045185 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045185/0 /scratch/stefan/7916127/working/building/REAL250005045185 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/307 `/scratch/stefan/7916127/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045185.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045185 none CC1CC1C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 104, 104, 49, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 104, 49, 49, 30, 30, 7, 1] 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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045185 none CC1CC1C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 67, 112, 189, 189, 189, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 13, 67, 67, 112, 112, 189, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045185 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045185 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045185/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045185 Building REAL250005045186 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045186' /scratch/stefan/7916127/working/building/REAL250005045186 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045186 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045186/0 /scratch/stefan/7916127/working/building/REAL250005045186 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/308 `/scratch/stefan/7916127/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045186.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045186 none CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [194, 194, 159, 194, 194, 114, 114, 114, 64, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 114, 64, 64, 36, 36, 9, 1, 194] 194 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]) total number of confs: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045186 none CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 79, 174, 174, 174, 194, 194, 194, 194, 194, 1, 2, 2, 2, 1, 1, 1, 7, 37, 37, 79, 79, 174, 194, 1] 194 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045186 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045186 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045186/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045186 Building REAL250005045187 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045187' /scratch/stefan/7916127/working/building/REAL250005045187 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045187 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045187/0 /scratch/stefan/7916127/working/building/REAL250005045187 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/309 `/scratch/stefan/7916127/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045187.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045187 none CCOCC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 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] 0 hydrogens need 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, 174, 110, 110, 110, 38, 23, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 174, 174, 110, 38, 38, 23, 23, 4, 1] 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]) total number of confs: 737 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045187 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045187 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045187/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045187 Building REAL250005045188 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045188' /scratch/stefan/7916127/working/building/REAL250005045188 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045188 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045188/0 /scratch/stefan/7916127/working/building/REAL250005045188 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/310 `/scratch/stefan/7916127/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045188.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045188 none CC(C)=CC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 92, 92, 92, 42, 31, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 92, 42, 42, 31, 31, 11, 1] 134 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]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045188 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045188 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045188/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045188 Building REAL250005045189 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045189' /scratch/stefan/7916127/working/building/REAL250005045189 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045189 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045189/0 /scratch/stefan/7916127/working/building/REAL250005045189 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/311 `/scratch/stefan/7916127/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=COCCO1)C1=CC(=O)[N-]O1) `REAL250005045189.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045189 none O=C(NCCNC(=O)C1=COCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 19, 30, 70, 70, 70, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 7, 19, 19, 30, 30, 70, 112, 112, 112, 112, 112, 1] 112 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 299 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: REAL250005045189 none O=C(NCCNC(=O)C1=COCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 63, 44, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 110, 112, 112, 112, 112, 112, 110, 63, 63, 44, 44, 12, 1, 1, 1, 1, 1, 112] 112 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 409 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045189 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045189 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045189/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045189 Building REAL250005045190 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045190' /scratch/stefan/7916127/working/building/REAL250005045190 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045190 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045190/0 /scratch/stefan/7916127/working/building/REAL250005045190 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/312 `/scratch/stefan/7916127/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=[N+]([O-])C=C1)C1=CC(=O)[N-]O1) `REAL250005045190.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045190 none O=C(NCCNC(=O)C1=CC=[N+]([O-])C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 32, 43, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 11, 32, 32, 43, 43, 71, 71, 71, 71, 71, 1] 71 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) 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: REAL250005045190 none O=C(NCCNC(=O)C1=CC=[N+]([O-])C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 3, 7, 3, 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, 65, 31, 15, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 65, 71, 71, 71, 71, 71, 65, 31, 31, 15, 15, 3, 1, 1, 1, 1, 71] 71 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045190 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045190 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045190/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045190 Building REAL250005045191 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045191' /scratch/stefan/7916127/working/building/REAL250005045191 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045191 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045191/0 /scratch/stefan/7916127/working/building/REAL250005045191 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/313 `/scratch/stefan/7916127/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2C=CC1C2)C1=CC(=O)[N-]O1) `REAL250005045191.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045191 none O=C(NCCNC(=O)C1CC2C=CC1C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 35, 52, 113, 113, 113, 164, 164, 164, 164, 164, 164, 1, 1, 1, 1, 1, 1, 11, 35, 35, 52, 52, 113, 164, 164, 164, 164, 164, 164, 164, 164, 164, 1] 164 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: 539 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: REAL250005045191 none O=C(NCCNC(=O)C1CC2C=CC1C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [154, 154, 79, 53, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 154, 164, 164, 164, 164, 164, 154, 79, 79, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164] 164 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 570 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045191 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045191 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045191/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045191 Building REAL250005045192 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045192' /scratch/stefan/7916127/working/building/REAL250005045192 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045192 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045192/0 /scratch/stefan/7916127/working/building/REAL250005045192 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/314 `/scratch/stefan/7916127/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045192.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045192 none CC(=O)NC(C)C(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 199, 106, 196, 106, 106, 41, 29, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 199, 196, 199, 106, 41, 41, 29, 29, 10, 1] 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]) total number of confs: 765 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045192 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045192 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045192/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045192 Building REAL250005045193 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045193' /scratch/stefan/7916127/working/building/REAL250005045193 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045193 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045193/0 /scratch/stefan/7916127/working/building/REAL250005045193 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/315 `/scratch/stefan/7916127/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NNC(=O)C=C1)C1=CC(=O)[N-]O1) `REAL250005045193.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045193 none O=C(NCCNC(=O)C1=NNC(=O)C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 38, 88, 88, 88, 150, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 1, 9, 31, 31, 38, 38, 88, 150, 150, 150, 1] 150 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005045193 none O=C(NCCNC(=O)C1=NNC(=O)C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [140, 138, 87, 63, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 138, 150, 150, 150, 150, 150, 140, 87, 87, 63, 63, 11, 1, 1, 1, 150] 150 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 559 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045193 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045193 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045193/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045193 Building REAL250005045194 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045194' /scratch/stefan/7916127/working/building/REAL250005045194 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045194 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045194/0 /scratch/stefan/7916127/working/building/REAL250005045194 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/316 `/scratch/stefan/7916127/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045194.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045194 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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, 75, 75, 75, 38, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 75, 38, 38, 24, 24, 9, 1] 87 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]) total number of confs: 287 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045194 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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, 6, 6, 7, 29, 48, 79, 79, 79, 87, 87, 87, 87, 87, 1, 2, 2, 2, 1, 1, 7, 29, 29, 48, 48, 79, 87] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 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/7916127/working/building/REAL250005045194 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045194 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045194/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045194 Building REAL250005045195 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045195' /scratch/stefan/7916127/working/building/REAL250005045195 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045195 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045195/0 /scratch/stefan/7916127/working/building/REAL250005045195 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/317 `/scratch/stefan/7916127/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045195.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045195 none O=C(CC1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 161, 201, 201, 201, 201, 201, 24, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 44, 24, 24, 16, 16, 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: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045195 none O=C(CC1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 29, 29, 110, 132, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 110, 110, 132, 132, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045195 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045195 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045195/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045195 Building REAL250005045196 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045196' /scratch/stefan/7916127/working/building/REAL250005045196 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045196 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045196/0 /scratch/stefan/7916127/working/building/REAL250005045196 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/318 `/scratch/stefan/7916127/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCO1)C1=CC(=O)[N-]O1) `REAL250005045196.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045196 none O=C(NCCNC(=O)C1CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 6, 22, 31, 71, 71, 71, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 7, 22, 22, 31, 31, 71, 117, 117, 117, 117, 117, 117, 117, 1] 117 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 385 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: REAL250005045196 none O=C(NCCNC(=O)C1CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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, 115, 82, 60, 12, 12, 1, 12, 1, 1, 1, 1, 1, 115, 117, 117, 117, 117, 117, 115, 82, 82, 60, 60, 12, 1, 1, 1, 1, 1, 1, 1, 117] 117 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 456 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045196 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045196 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045196/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045196 Building REAL250005045197 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045197' /scratch/stefan/7916127/working/building/REAL250005045197 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045197 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045197/0 /scratch/stefan/7916127/working/building/REAL250005045197 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/319 `/scratch/stefan/7916127/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045197.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045197 none CSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 101, 101, 101, 44, 24, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 187, 187, 101, 44, 44, 24, 24, 6, 1] 201 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]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045197 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045197 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045197/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045197 Building REAL250005045198 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045198' /scratch/stefan/7916127/working/building/REAL250005045198 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045198 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045198/0 /scratch/stefan/7916127/working/building/REAL250005045198 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/320 `/scratch/stefan/7916127/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005045198.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045198 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 78, 78, 78, 37, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 78, 37, 37, 24, 24, 9, 1] 84 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]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045198 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 26, 39, 78, 78, 78, 84, 84, 84, 84, 84, 1, 1, 2, 2, 2, 1, 8, 26, 26, 39, 39, 78, 84] 84 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 288 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045198 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045198 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045198/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045198 Building REAL250005045199 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045199' /scratch/stefan/7916127/working/building/REAL250005045199 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045199 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045199/0 /scratch/stefan/7916127/working/building/REAL250005045199 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/321 `/scratch/stefan/7916127/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045199.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045199 none CSCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 154, 148, 74, 74, 74, 31, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 155, 155, 149, 149, 74, 31, 31, 18, 18, 4, 1] 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]) total number of confs: 730 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045199 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045199 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045199/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045199 Building REAL250005045200 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045200' /scratch/stefan/7916127/working/building/REAL250005045200 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045200 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045200/0 /scratch/stefan/7916127/working/building/REAL250005045200 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/322 `/scratch/stefan/7916127/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045200.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045200 none CC(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 190, 201, 175, 76, 76, 76, 30, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 198, 201, 201, 201, 201, 191, 191, 176, 176, 76, 30, 30, 20, 20, 4, 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: 850 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045200 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045200 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045200/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045200 Building REAL250005045201 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045201' /scratch/stefan/7916127/working/building/REAL250005045201 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045201 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045201/0 /scratch/stefan/7916127/working/building/REAL250005045201 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/323 `/scratch/stefan/7916127/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=C1) `REAL250005045201.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045201 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 29, 63, 125, 125, 125, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 5, 29, 29, 63, 63, 125, 135, 1, 1, 1] 135 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 490 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045201 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 47, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 98, 135, 135, 135, 135, 98, 47, 47, 30, 30, 9, 1, 135, 135, 135] 135 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 414 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045201 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045201 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045201/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045201 Building REAL250005045202 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045202' /scratch/stefan/7916127/working/building/REAL250005045202 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045202 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045202/0 /scratch/stefan/7916127/working/building/REAL250005045202 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/324 `/scratch/stefan/7916127/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CO1) `REAL250005045202.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045202 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CO1 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.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 116, 116, 116, 54, 34, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 116, 54, 54, 34, 34, 8, 1, 189, 189] 189 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]) total number of confs: 512 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045202 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CO1 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.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 50, 94, 181, 181, 181, 189, 189, 189, 189, 189, 1, 1, 1, 2, 2, 2, 9, 50, 50, 94, 94, 181, 189, 1, 1] 189 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045202 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045202 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045202/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045202 Building REAL250005045203 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045203' /scratch/stefan/7916127/working/building/REAL250005045203 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045203 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045203/0 /scratch/stefan/7916127/working/building/REAL250005045203 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/325 `/scratch/stefan/7916127/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1C=CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045203.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045203 none O=C(CC1C=CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 176, 201, 201, 201, 201, 39, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 201, 201, 201, 201, 84, 39, 39, 23, 23, 4, 1] 201 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: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045203 none O=C(CC1C=CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 32, 32, 100, 130, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 32, 100, 100, 130, 130, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045203 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045203 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045203/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045203 Building REAL250005045204 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045204' /scratch/stefan/7916127/working/building/REAL250005045204 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045204 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045204/0 /scratch/stefan/7916127/working/building/REAL250005045204 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/326 `/scratch/stefan/7916127/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=NN=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045204.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045204 none O=C(CN1C=NN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 152, 201, 201, 201, 199, 27, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 152, 152, 201, 70, 27, 27, 18, 18, 6, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL250005045204 none O=C(CN1C=NN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 50, 50, 135, 156, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 50, 135, 135, 156, 156, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 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/7916127/working/building/REAL250005045204 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045204 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045204/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045204 Building REAL250005045205 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045205' /scratch/stefan/7916127/working/building/REAL250005045205 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045205 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045205/0 /scratch/stefan/7916127/working/building/REAL250005045205 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/327 `/scratch/stefan/7916127/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCCC1=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045205.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045205 none O=C(CN1CCCC1=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [113, 113, 113, 161, 176, 176, 176, 176, 176, 39, 25, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 161, 161, 176, 176, 176, 176, 176, 176, 113, 39, 39, 25, 25, 5, 1] 176 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: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045205 none O=C(CN1CCCC1=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [30, 8, 1, 1, 1, 1, 1, 1, 1, 30, 30, 87, 114, 175, 176, 175, 176, 176, 176, 176, 176, 8, 8, 1, 1, 1, 1, 1, 1, 30, 87, 87, 114, 114, 176, 176] 176 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045205 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045205 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045205/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045205 Building REAL250005045206 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045206' /scratch/stefan/7916127/working/building/REAL250005045206 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045206 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045206/0 /scratch/stefan/7916127/working/building/REAL250005045206 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/328 `/scratch/stefan/7916127/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1) `REAL250005045206.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045206 none CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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, 89, 89, 90, 48, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 90, 48, 48, 32, 32, 11, 1, 111] 111 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]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045206 none CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 27, 48, 103, 103, 103, 111, 111, 111, 111, 111, 1, 1, 2, 2, 2, 1, 5, 27, 27, 48, 48, 103, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 387 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045206 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045206 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045206/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045206 Building REAL250005045207 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045207' /scratch/stefan/7916127/working/building/REAL250005045207 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045207 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045207/0 /scratch/stefan/7916127/working/building/REAL250005045207 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/329 `/scratch/stefan/7916127/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045207.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045207 none CC1=NOC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 99, 99, 99, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 99, 33, 33, 20, 20, 4, 1] 201 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]) total number of confs: 480 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: REAL250005045207 none CC1=NOC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 62, 97, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 2, 2, 2, 11, 62, 62, 97, 97, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 738 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045207 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045207 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045207/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045207 Building REAL250005045208 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045208' /scratch/stefan/7916127/working/building/REAL250005045208 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045208 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045208/0 /scratch/stefan/7916127/working/building/REAL250005045208 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/330 `/scratch/stefan/7916127/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SN=N1) `REAL250005045208.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045208 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SN=N1 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', 'S.3', 'N.2', 'N.2', '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, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 127, 127, 127, 58, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 127, 58, 58, 32, 32, 11, 1] 201 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]) total number of confs: 547 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045208 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SN=N1 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', 'S.3', 'N.2', 'N.2', '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, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 55, 97, 191, 191, 191, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 55, 55, 97, 97, 191, 201] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 723 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045208 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045208 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045208/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045208 Building REAL250005045209 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045209' /scratch/stefan/7916127/working/building/REAL250005045209 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045209 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045209/0 /scratch/stefan/7916127/working/building/REAL250005045209 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/331 `/scratch/stefan/7916127/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)O1) `REAL250005045209.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045209 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 143, 97, 97, 97, 40, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 97, 40, 40, 26, 26, 9, 1, 143, 143, 143] 143 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]) total number of confs: 392 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: REAL250005045209 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 56, 85, 139, 139, 139, 143, 143, 143, 143, 143, 1, 1, 1, 2, 2, 2, 1, 11, 56, 56, 85, 85, 139, 143, 2, 2, 2] 143 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 550 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045209 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045209 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045209/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045209 Building REAL250005045210 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045210' /scratch/stefan/7916127/working/building/REAL250005045210 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045210 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045210/0 /scratch/stefan/7916127/working/building/REAL250005045210 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/332 `/scratch/stefan/7916127/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC=CCC1)C1=CC(=O)[N-]O1) `REAL250005045210.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045210 none O=C(NCCNC(=O)C1CC=CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [11, 1, 11, 11, 37, 60, 127, 127, 127, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 11, 37, 37, 60, 60, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 683 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: REAL250005045210 none O=C(NCCNC(=O)C1CC=CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [185, 184, 103, 61, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 184, 201, 201, 201, 201, 201, 185, 103, 103, 61, 61, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 722 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045210 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045210 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045210/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045210 Building REAL250005045211 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045211' /scratch/stefan/7916127/working/building/REAL250005045211 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045211 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045211/0 /scratch/stefan/7916127/working/building/REAL250005045211 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/333 `/scratch/stefan/7916127/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045211.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045211 none O=C(CCC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 111, 141, 201, 201, 201, 201, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 111, 111, 141, 141, 201, 201, 201, 41, 17, 17, 10, 10, 2, 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: 706 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045211 none O=C(CCC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 10, 4, 1, 1, 1, 1, 1, 1, 46, 46, 140, 161, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 4, 4, 1, 1, 1, 46, 144, 144, 159, 159, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 795 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045211 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045211 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045211/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045211 Building REAL250005045212 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045212' /scratch/stefan/7916127/working/building/REAL250005045212 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045212 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045212/0 /scratch/stefan/7916127/working/building/REAL250005045212 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/334 `/scratch/stefan/7916127/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045212.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045212 none CC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [102, 102, 102, 102, 78, 78, 78, 39, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 102, 102, 102, 102, 78, 39, 39, 25, 25, 9, 1, 102] 102 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]) total number of confs: 311 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045212 none CC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 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 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, 1, 6, 6, 6, 30, 49, 97, 97, 97, 102, 102, 102, 102, 102, 1, 2, 2, 2, 6, 30, 30, 50, 50, 97, 102, 1] 102 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 388 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045212 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045212 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045212/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045212 Building REAL250005045213 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045213' /scratch/stefan/7916127/working/building/REAL250005045213 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045213 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045213/0 /scratch/stefan/7916127/working/building/REAL250005045213 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/335 `/scratch/stefan/7916127/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CN1) `REAL250005045213.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045213 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 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: [10, 1, 10, 10, 40, 60, 100, 100, 100, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 10, 40, 40, 60, 60, 100, 108, 1, 1, 1, 1] 108 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045213 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 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: [85, 85, 45, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 85, 108, 108, 108, 108, 85, 45, 45, 30, 30, 11, 1, 108, 108, 108, 108] 108 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 338 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045213 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045213 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045213/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045213 Building REAL250005045214 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045214' /scratch/stefan/7916127/working/building/REAL250005045214 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045214 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045214/0 /scratch/stefan/7916127/working/building/REAL250005045214 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/336 `/scratch/stefan/7916127/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(Cl)=CN1) `REAL250005045214.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045214 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(Cl)=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [10, 1, 10, 10, 44, 66, 109, 109, 109, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 10, 44, 44, 66, 66, 109, 117, 1, 1, 1] 117 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 429 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045214 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(Cl)=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 16, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [87, 87, 40, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 87, 117, 117, 117, 117, 117, 87, 40, 40, 26, 26, 9, 1, 117, 117, 117] 117 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]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045214 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045214 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045214/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045214 Building REAL250005045215 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045215' /scratch/stefan/7916127/working/building/REAL250005045215 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045215 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045215/0 /scratch/stefan/7916127/working/building/REAL250005045215 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/337 `/scratch/stefan/7916127/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045215.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045215 none CC(=O)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 49, 77, 40, 41, 28, 28, 28, 17, 16, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 77, 77, 77, 47, 47, 47, 47, 41, 41, 28, 17, 17, 16, 16, 8, 1] 77 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: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045215 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045215 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045215/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045215 Building REAL250005045216 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045216' /scratch/stefan/7916127/working/building/REAL250005045216 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045216 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045216/0 /scratch/stefan/7916127/working/building/REAL250005045216 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/338 `/scratch/stefan/7916127/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1C) `REAL250005045216.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045216 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.pl3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 131, 131, 131, 57, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 178, 178, 178, 178, 178, 178, 178, 131, 57, 57, 36, 36, 9, 1, 178, 178, 178] 178 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]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045216 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'N.pl3', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 10, 57, 97, 168, 168, 168, 178, 178, 178, 178, 178, 1, 1, 2, 2, 2, 1, 1, 10, 57, 57, 97, 97, 168, 178, 2, 2, 2] 178 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 659 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045216 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045216 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045216/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045216 Building REAL250005045217 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045217' /scratch/stefan/7916127/working/building/REAL250005045217 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045217 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045217/0 /scratch/stefan/7916127/working/building/REAL250005045217 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/339 `/scratch/stefan/7916127/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC=C1) `REAL250005045217.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045217 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [5, 1, 5, 5, 31, 58, 111, 111, 111, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 5, 31, 31, 58, 58, 111, 119, 1, 1, 1] 119 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045217 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [79, 79, 45, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 79, 119, 119, 119, 119, 79, 45, 45, 29, 29, 9, 1, 119, 119, 119] 119 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045217 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045217 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045217/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045217 Building REAL250005045218 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045218' /scratch/stefan/7916127/working/building/REAL250005045218 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045218 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045218/0 /scratch/stefan/7916127/working/building/REAL250005045218 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/340 `/scratch/stefan/7916127/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045218.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045218 none O=C(CN1C=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 109, 109, 177, 201, 201, 201, 201, 40, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 201, 109, 40, 40, 25, 25, 4, 1] 201 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]) 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: REAL250005045218 none O=C(CN1C=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 35, 35, 91, 136, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 35, 91, 91, 136, 136, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045218 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045218 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045218/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045218 Building REAL250005045219 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045219' /scratch/stefan/7916127/working/building/REAL250005045219 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045219 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045219/0 /scratch/stefan/7916127/working/building/REAL250005045219 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/341 `/scratch/stefan/7916127/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=C1) `REAL250005045219.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045219 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=C1 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', 'O.3', 'C.2', 'C.2', '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, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 127, 127, 127, 60, 37, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 158, 158, 158, 158, 158, 158, 127, 60, 60, 37, 37, 9, 1, 158, 158] 158 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]) total number of confs: 479 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045219 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=C1 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', 'O.3', 'C.2', 'C.2', '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, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 45, 84, 148, 148, 148, 158, 158, 158, 158, 158, 1, 1, 1, 2, 2, 2, 8, 45, 45, 84, 84, 148, 158, 1, 1] 158 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045219 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045219 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045219/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045219 Building REAL250005045220 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045220' /scratch/stefan/7916127/working/building/REAL250005045220 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045220 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045220/0 /scratch/stefan/7916127/working/building/REAL250005045220 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/342 `/scratch/stefan/7916127/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2CCC1C2)C1=CC(=O)[N-]O1) `REAL250005045220.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045220 none O=C(NCCNC(=O)C1CC2CCC1C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 31, 43, 91, 91, 91, 110, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 10, 31, 31, 43, 43, 91, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 1] 110 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: 376 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045220 none O=C(NCCNC(=O)C1CC2CCC1C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 46, 28, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 103, 110, 110, 110, 110, 110, 103, 46, 46, 28, 28, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 110] 110 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 372 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045220 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045220 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045220/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045220 Building REAL250005045221 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045221' /scratch/stefan/7916127/working/building/REAL250005045221 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045221 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045221/0 /scratch/stefan/7916127/working/building/REAL250005045221 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/343 `/scratch/stefan/7916127/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(Cl)O1) `REAL250005045221.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045221 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 16, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 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: [7, 1, 7, 6, 31, 48, 85, 85, 85, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 7, 31, 31, 48, 48, 85, 93, 1, 1] 93 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 340 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045221 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(Cl)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 16, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 3, 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: [81, 81, 42, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 81, 93, 93, 93, 93, 93, 81, 42, 42, 26, 26, 9, 1, 93, 93] 93 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]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045221 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045221 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045221/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045221 Building REAL250005045222 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045222' /scratch/stefan/7916127/working/building/REAL250005045222 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045222 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045222/0 /scratch/stefan/7916127/working/building/REAL250005045222 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/344 `/scratch/stefan/7916127/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NN1C) `REAL250005045222.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045222 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NN1C 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.2', 'N.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 116, 116, 116, 47, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 184, 116, 47, 47, 31, 31, 9, 1, 184, 184, 184, 184] 184 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: 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: REAL250005045222 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NN1C 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.2', 'N.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 53, 95, 182, 182, 182, 184, 184, 184, 184, 184, 1, 1, 1, 1, 2, 2, 2, 9, 53, 53, 95, 95, 182, 184, 1, 2, 2, 2] 184 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 680 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045222 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045222 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045222/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045222 Building REAL250005045223 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045223' /scratch/stefan/7916127/working/building/REAL250005045223 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045223 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045223/0 /scratch/stefan/7916127/working/building/REAL250005045223 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/345 `/scratch/stefan/7916127/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045223.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045223 none CCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 177, 163, 135, 53, 53, 53, 21, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 179, 179, 165, 165, 135, 135, 53, 21, 21, 14, 14, 4, 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: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045223 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045223 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045223/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045223 Building REAL250005045224 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045224' /scratch/stefan/7916127/working/building/REAL250005045224 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045224 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045224/0 /scratch/stefan/7916127/working/building/REAL250005045224 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/346 `/scratch/stefan/7916127/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045224.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045224 none CC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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, 134, 138, 140, 93, 93, 93, 47, 30, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 140, 140, 136, 136, 93, 47, 47, 30, 30, 9, 1] 140 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: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045224 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045224 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045224/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045224 Building REAL250005045225 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045225' /scratch/stefan/7916127/working/building/REAL250005045225 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045225 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045225/0 /scratch/stefan/7916127/working/building/REAL250005045225 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/347 `/scratch/stefan/7916127/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1) `REAL250005045225.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045225 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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, 114, 89, 89, 89, 48, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 114, 114, 114, 114, 114, 114, 114, 89, 48, 48, 33, 33, 11, 1, 114] 114 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]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045225 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 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: [1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 54, 108, 108, 108, 114, 114, 114, 114, 114, 1, 1, 2, 2, 2, 1, 1, 7, 31, 31, 54, 54, 108, 114, 1] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045225 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045225 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045225/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045225 Building REAL250005045226 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045226' /scratch/stefan/7916127/working/building/REAL250005045226 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045226 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045226/0 /scratch/stefan/7916127/working/building/REAL250005045226 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/348 `/scratch/stefan/7916127/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045226.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045226 none CN1C=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 88, 88, 88, 43, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 116, 88, 43, 43, 26, 26, 7, 1] 116 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]) 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: REAL250005045226 none CN1C=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 42, 57, 112, 112, 112, 116, 116, 116, 116, 116, 2, 2, 2, 1, 1, 1, 10, 42, 42, 57, 57, 112, 116] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045226 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045226 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045226/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045226 Building REAL250005045227 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045227' /scratch/stefan/7916127/working/building/REAL250005045227 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045227 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045227/0 /scratch/stefan/7916127/working/building/REAL250005045227 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/349 `/scratch/stefan/7916127/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045227.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045227 none O=C(CCN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 144, 171, 201, 201, 201, 201, 30, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 144, 144, 171, 171, 201, 201, 79, 30, 30, 21, 21, 4, 1] 201 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]) total number of confs: 731 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045227 none O=C(CCN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 16, 8, 1, 1, 1, 1, 1, 1, 70, 70, 135, 156, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 8, 8, 1, 1, 70, 137, 137, 155, 155, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045227 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045227 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045227/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045227 Building REAL250005045228 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045228' /scratch/stefan/7916127/working/building/REAL250005045228 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045228 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045228/0 /scratch/stefan/7916127/working/building/REAL250005045228 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/350 `/scratch/stefan/7916127/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045228.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045228 none CCCCC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 182, 166, 68, 68, 68, 27, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 182, 183, 168, 168, 68, 27, 27, 18, 18, 4, 1] 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]) total number of confs: 875 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045228 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045228 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045228/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045228 Building REAL250005045229 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045229' /scratch/stefan/7916127/working/building/REAL250005045229 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045229 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045229/0 /scratch/stefan/7916127/working/building/REAL250005045229 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/351 `/scratch/stefan/7916127/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045229.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045229 none CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 85, 85, 41, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 41, 41, 30, 30, 7, 1] 85 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]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045229 none CC1=CC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 25, 42, 83, 83, 83, 85, 85, 85, 85, 85, 1, 2, 2, 2, 1, 1, 1, 4, 25, 25, 42, 42, 83, 85] 85 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 311 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045229 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045229 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045229/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045229 Building REAL250005045230 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045230' /scratch/stefan/7916127/working/building/REAL250005045230 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045230 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045230/0 /scratch/stefan/7916127/working/building/REAL250005045230 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/352 `/scratch/stefan/7916127/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045230.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045230 none O=C(CCN1C=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 129, 155, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 129, 129, 155, 155, 201, 201, 201, 64, 23, 23, 14, 14, 4, 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: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045230 none O=C(CCN1C=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 18, 8, 1, 1, 1, 1, 1, 1, 74, 74, 140, 162, 201, 201, 201, 201, 201, 201, 201, 201, 18, 18, 8, 8, 1, 1, 1, 74, 142, 142, 161, 161, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045230 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045230 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045230/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045230 Building REAL250005045231 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045231' /scratch/stefan/7916127/working/building/REAL250005045231 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045231 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045231/0 /scratch/stefan/7916127/working/building/REAL250005045231 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/353 `/scratch/stefan/7916127/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC=C1O)C1=CC(=O)[N-]O1) `REAL250005045231.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045231 none O=C(NCCNC(=O)C1=CC=CC=C1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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 292 conformations in input total number of sets (complete confs): 292 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 43, 95, 95, 95, 146, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 8, 28, 28, 43, 43, 95, 146, 146, 146, 146, 292, 1] 292 rigid atoms, others: [32, 1, 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]) total number of confs: 691 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: REAL250005045231 none O=C(NCCNC(=O)C1=CC=CC=C1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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 292 conformations in input total number of sets (complete confs): 292 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 66, 44, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 142, 146, 146, 146, 146, 146, 142, 66, 66, 44, 44, 10, 1, 1, 1, 1, 2, 146] 292 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 520 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045231 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045231 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045231/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045231 Building REAL250005045232 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045232' /scratch/stefan/7916127/working/building/REAL250005045232 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045232 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045232/0 /scratch/stefan/7916127/working/building/REAL250005045232 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/354 `/scratch/stefan/7916127/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045232.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045232 none CCC(C)C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 98, 177, 98, 98, 42, 27, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 177, 177, 98, 42, 42, 27, 27, 7, 1] 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]) total number of confs: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045232 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045232 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045232/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045232 Building REAL250005045233 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045233' /scratch/stefan/7916127/working/building/REAL250005045233 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045233 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045233/0 /scratch/stefan/7916127/working/building/REAL250005045233 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/355 `/scratch/stefan/7916127/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)SCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045233.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045233 none CC(C)SCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 201, 115, 63, 63, 63, 21, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 115, 115, 63, 21, 21, 12, 12, 4, 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: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045233 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045233 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045233/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045233 Building REAL250005045234 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045234' /scratch/stefan/7916127/working/building/REAL250005045234 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045234 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045234/0 /scratch/stefan/7916127/working/building/REAL250005045234 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/356 `/scratch/stefan/7916127/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045234.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045234 none N#CCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 182, 111, 55, 55, 55, 21, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 111, 111, 55, 21, 21, 12, 12, 4, 1] 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]) total number of confs: 644 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045234 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045234 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045234/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045234 Building REAL250005045235 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045235' /scratch/stefan/7916127/working/building/REAL250005045235 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045235 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045235/0 /scratch/stefan/7916127/working/building/REAL250005045235 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/357 `/scratch/stefan/7916127/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045235.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045235 none CC(=O)N(C)CC(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [173, 165, 173, 149, 165, 80, 80, 80, 37, 28, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 173, 173, 173, 165, 165, 165, 149, 149, 80, 37, 37, 28, 28, 7, 1] 173 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: 635 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045235 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045235 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045235/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045235 Building REAL250005045236 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045236' /scratch/stefan/7916127/working/building/REAL250005045236 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045236 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045236/0 /scratch/stefan/7916127/working/building/REAL250005045236 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/358 `/scratch/stefan/7916127/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045236.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045236 none CCC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 151, 104, 151, 184, 104, 104, 37, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 187, 187, 187, 187, 187, 151, 185, 185, 185, 185, 185, 104, 37, 37, 20, 20, 4, 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: 1021 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045236 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045236 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045236/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045236 Building REAL250005045237 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045237' /scratch/stefan/7916127/working/building/REAL250005045237 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045237 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045237/0 /scratch/stefan/7916127/working/building/REAL250005045237 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/359 `/scratch/stefan/7916127/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045237.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045237 none CC(C)OCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 143, 201, 115, 101, 41, 41, 41, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 115, 115, 101, 101, 41, 25, 25, 16, 16, 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: 887 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045237 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045237 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045237/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045237 Building REAL250005045238 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045238' /scratch/stefan/7916127/working/building/REAL250005045238 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045238 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045238/0 /scratch/stefan/7916127/working/building/REAL250005045238 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/360 `/scratch/stefan/7916127/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045238.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045238 none CCC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need 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, 145, 116, 116, 116, 43, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 145, 116, 43, 43, 29, 29, 7, 1, 145] 201 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]) total number of confs: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045238 none CCC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 11, 11, 11, 35, 60, 135, 135, 135, 145, 145, 145, 145, 145, 1, 8, 8, 8, 8, 8, 1, 11, 35, 35, 60, 60, 135, 145, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 500 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045238 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045238 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045238/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045238 Building REAL250005045239 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045239' /scratch/stefan/7916127/working/building/REAL250005045239 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045239 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045239/0 /scratch/stefan/7916127/working/building/REAL250005045239 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/361 `/scratch/stefan/7916127/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045239.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045239 none O=C(CCC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 129, 129, 201, 201, 201, 201, 27, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 130, 130, 159, 158, 201, 201, 201, 201, 201, 201, 201, 60, 27, 27, 18, 18, 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: 923 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045239 none O=C(CCC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 14, 7, 1, 1, 1, 1, 1, 1, 55, 55, 133, 163, 200, 201, 201, 201, 201, 201, 201, 201, 14, 14, 7, 7, 1, 1, 1, 1, 1, 1, 1, 55, 133, 133, 163, 163, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045239 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045239 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045239/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045239 Building REAL250005045240 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045240' /scratch/stefan/7916127/working/building/REAL250005045240 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045240 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045240/0 /scratch/stefan/7916127/working/building/REAL250005045240 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/362 `/scratch/stefan/7916127/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1COCCO1)C1=CC(=O)[N-]O1) `REAL250005045240.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045240 none O=C(NCCNC(=O)C1COCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 6, 24, 34, 82, 82, 82, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 7, 24, 24, 34, 34, 82, 137, 137, 137, 137, 137, 137, 137, 1] 137 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045240 none O=C(NCCNC(=O)C1COCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 87, 61, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 133, 137, 137, 137, 137, 137, 133, 87, 87, 61, 61, 13, 1, 1, 1, 1, 1, 1, 1, 137] 137 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045240 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045240 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045240/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045240 Building REAL250005045241 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045241' /scratch/stefan/7916127/working/building/REAL250005045241 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045241 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045241/0 /scratch/stefan/7916127/working/building/REAL250005045241 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/363 `/scratch/stefan/7916127/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=NN1) `REAL250005045241.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045241 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 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: [7, 1, 7, 6, 27, 42, 71, 71, 71, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 7, 27, 27, 42, 42, 71, 79, 1, 1, 1] 79 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045241 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 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: [65, 65, 35, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 65, 79, 79, 79, 79, 65, 35, 35, 24, 24, 9, 1, 79, 79, 79] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045241 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045241 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045241/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045241 Building REAL250005045242 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045242' /scratch/stefan/7916127/working/building/REAL250005045242 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045242 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045242/0 /scratch/stefan/7916127/working/building/REAL250005045242 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/364 `/scratch/stefan/7916127/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CC=N1) `REAL250005045242.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045242 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CC=N1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 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: [10, 1, 10, 33, 33, 33, 80, 89, 101, 101, 101, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 10, 10, 10, 10, 33, 80, 80, 89, 89, 101, 101, 1, 1, 1] 101 rigid atoms, others: [32, 1, 34, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 384 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045242 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CC=N1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 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: [86, 50, 50, 50, 20, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 86, 101, 101, 101, 101, 86, 86, 86, 86, 50, 20, 20, 15, 15, 5, 1, 101, 101, 101] 101 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045242 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045242 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045242/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045242 Building REAL250005045243 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045243' /scratch/stefan/7916127/working/building/REAL250005045243 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045243 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045243/0 /scratch/stefan/7916127/working/building/REAL250005045243 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/365 `/scratch/stefan/7916127/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045243.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045243 none CCCCC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 167, 148, 94, 35, 94, 105, 35, 35, 24, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 196, 195, 196, 196, 196, 165, 167, 150, 150, 94, 119, 119, 119, 119, 119, 35, 24, 24, 15, 15, 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: 1190 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045243 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045243 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045243/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045243 Building REAL250005045244 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045244' /scratch/stefan/7916127/working/building/REAL250005045244 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045244 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045244/0 /scratch/stefan/7916127/working/building/REAL250005045244 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/366 `/scratch/stefan/7916127/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045244.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045244 none CSC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 91, 164, 91, 91, 35, 23, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 164, 164, 164, 164, 91, 35, 35, 23, 23, 5, 1] 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]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045244 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045244 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045244/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045244 Building REAL250005045245 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045245' /scratch/stefan/7916127/working/building/REAL250005045245 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045245 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045245/0 /scratch/stefan/7916127/working/building/REAL250005045245 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/367 `/scratch/stefan/7916127/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045245.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045245 none CCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 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] 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, 193, 183, 128, 185, 128, 128, 43, 26, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 185, 185, 185, 185, 128, 43, 43, 26, 26, 7, 1] 197 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: 741 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045245 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045245 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045245/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045245 Building REAL250005045246 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045246' /scratch/stefan/7916127/working/building/REAL250005045246 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045246 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045246/0 /scratch/stefan/7916127/working/building/REAL250005045246 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/368 `/scratch/stefan/7916127/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045246.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045246 none CC(C)COCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 201, 186, 169, 169, 68, 68, 68, 24, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 194, 194, 171, 171, 171, 171, 68, 24, 24, 17, 17, 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: 802 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045246 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045246 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045246/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045246 Building REAL250005045247 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045247' /scratch/stefan/7916127/working/building/REAL250005045247 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045247 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045247/0 /scratch/stefan/7916127/working/building/REAL250005045247 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/369 `/scratch/stefan/7916127/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045247.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045247 none CCOCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 177, 135, 133, 132, 72, 72, 72, 31, 24, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 134, 135, 135, 134, 134, 72, 31, 31, 24, 24, 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: 752 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045247 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045247 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045247/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045247 Building REAL250005045248 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045248' /scratch/stefan/7916127/working/building/REAL250005045248 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045248 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045248/0 /scratch/stefan/7916127/working/building/REAL250005045248 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/370 `/scratch/stefan/7916127/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045248.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045248 none O=C(COCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 71, 107, 156, 201, 201, 16, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 71, 71, 156, 156, 201, 201, 201, 201, 201, 34, 16, 16, 11, 11, 3, 1] 201 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: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045248 none O=C(COCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 57, 24, 9, 1, 1, 1, 1, 105, 105, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 57, 57, 9, 9, 1, 1, 1, 1, 1, 105, 172, 172, 172, 172, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045248 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045248 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045248/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045248 Building REAL250005045249 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045249' /scratch/stefan/7916127/working/building/REAL250005045249 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045249 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045249/0 /scratch/stefan/7916127/working/building/REAL250005045249 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/371 `/scratch/stefan/7916127/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045249.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045249 none O=C(CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 177, 201, 201, 201, 201, 35, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 201, 201, 201, 201, 91, 35, 35, 20, 20, 4, 1] 201 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: 770 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045249 none O=C(CC1CCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 30, 30, 93, 128, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 30, 93, 93, 128, 128, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 787 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045249 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045249 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045249/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045249 Building REAL250005045250 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045250' /scratch/stefan/7916127/working/building/REAL250005045250 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045250 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045250/0 /scratch/stefan/7916127/working/building/REAL250005045250 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/372 `/scratch/stefan/7916127/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SC=N1) `REAL250005045250.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045250 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SC=N1 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', 'S.3', 'C.2', 'N.2', '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, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 120, 120, 120, 51, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 120, 51, 51, 30, 30, 7, 1, 201] 201 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]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045250 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)SC=N1 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', 'S.3', 'C.2', 'N.2', '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, 14, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 57, 98, 194, 194, 194, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 57, 57, 98, 98, 194, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045250 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045250 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045250/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045250 Building REAL250005045251 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045251' /scratch/stefan/7916127/working/building/REAL250005045251 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045251 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045251/0 /scratch/stefan/7916127/working/building/REAL250005045251 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/373 `/scratch/stefan/7916127/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNN=C1) `REAL250005045251.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045251 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 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: [5, 1, 5, 5, 17, 29, 57, 57, 57, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 5, 17, 17, 29, 29, 57, 61, 1, 1, 1] 61 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 207 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045251 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 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, 41, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 41, 41, 28, 28, 8, 1, 61, 61, 61] 61 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28]) total number of confs: 232 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045251 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045251 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045251/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045251 Building REAL250005045252 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045252' /scratch/stefan/7916127/working/building/REAL250005045252 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045252 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045252/0 /scratch/stefan/7916127/working/building/REAL250005045252 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/374 `/scratch/stefan/7916127/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CNC(=O)C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045252.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045252 none O=C(CNC(=O)C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 71, 105, 105, 105, 201, 201, 17, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 71, 105, 201, 201, 201, 201, 201, 43, 17, 17, 14, 14, 4, 1] 201 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: 696 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: REAL250005045252 none O=C(CNC(=O)C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 8, 1, 11, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 4, 7, 6, 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] 0 hydrogens 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, 31, 9, 9, 1, 9, 1, 1, 1, 61, 61, 141, 147, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 9, 1, 1, 1, 1, 1, 61, 141, 141, 147, 147, 201, 201] 201 rigid atoms, others: [4, 6, 7, 8, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 733 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045252 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045252 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045252/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045252 Building REAL250005045253 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045253' /scratch/stefan/7916127/working/building/REAL250005045253 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045253 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045253/0 /scratch/stefan/7916127/working/building/REAL250005045253 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/375 `/scratch/stefan/7916127/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045253.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045253 none COCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 173, 151, 67, 67, 67, 31, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 195, 195, 181, 181, 151, 151, 67, 31, 31, 18, 18, 4, 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: 879 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045253 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045253 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045253/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045253 Building REAL250005045254 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045254' /scratch/stefan/7916127/working/building/REAL250005045254 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045254 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045254/0 /scratch/stefan/7916127/working/building/REAL250005045254 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/376 `/scratch/stefan/7916127/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045254.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045254 none O=C(COC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 127, 177, 201, 201, 201, 201, 20, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 127, 127, 201, 201, 201, 201, 201, 201, 201, 201, 201, 66, 20, 20, 11, 11, 3, 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: 681 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045254 none O=C(COC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 3, 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, 7, 7, 7] 0 hydrogens 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, 16, 5, 1, 1, 1, 1, 1, 1, 48, 48, 114, 126, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 114, 114, 126, 126, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 731 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045254 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045254 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045254/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045254 Building REAL250005045255 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045255' /scratch/stefan/7916127/working/building/REAL250005045255 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045255 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045255/0 /scratch/stefan/7916127/working/building/REAL250005045255 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/377 `/scratch/stefan/7916127/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045255.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045255 none CC1=NC=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 190, 201, 201, 116, 116, 116, 47, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 116, 47, 47, 34, 34, 9, 1] 201 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: 573 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045255 none CC1=NC=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 65, 111, 191, 193, 191, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 10, 65, 65, 111, 111, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045255 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045255 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045255/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045255 Building REAL250005045256 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045256' /scratch/stefan/7916127/working/building/REAL250005045256 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045256 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045256/0 /scratch/stefan/7916127/working/building/REAL250005045256 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/378 `/scratch/stefan/7916127/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCSCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045256.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045256 none CCSCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 113, 109, 36, 36, 36, 18, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 113, 113, 109, 109, 36, 18, 18, 11, 11, 3, 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: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045256 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045256 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045256/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045256 Building REAL250005045257 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045257' /scratch/stefan/7916127/working/building/REAL250005045257 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045257 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045257/0 /scratch/stefan/7916127/working/building/REAL250005045257 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/379 `/scratch/stefan/7916127/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045257.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045257 none CCOC1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 147, 147, 147, 60, 60, 60, 23, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 147, 147, 147, 147, 60, 23, 23, 13, 13, 4, 1] 201 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: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045257 none CCOC1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 12, 12, 12, 52, 68, 139, 141, 139, 147, 147, 147, 147, 147, 10, 10, 10, 10, 10, 1, 1, 1, 1, 12, 52, 52, 68, 68, 141, 147] 201 rigid atoms, others: [2, 3, 4, 5, 6, 25, 26, 27, 28] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 551 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045257 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045257 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045257/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045257 Building REAL250005045258 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045258' /scratch/stefan/7916127/working/building/REAL250005045258 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045258 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045258/0 /scratch/stefan/7916127/working/building/REAL250005045258 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/380 `/scratch/stefan/7916127/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NSN=C1) `REAL250005045258.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045258 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NSN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 14, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [5, 1, 5, 5, 21, 34, 73, 73, 73, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 5, 21, 21, 34, 34, 73, 79, 1] 79 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045258 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NSN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'S.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 14, 8, 1, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 45, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 77, 79, 79, 79, 79, 77, 45, 45, 30, 30, 9, 1, 79] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045258 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045258 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045258/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045258 Building REAL250005045259 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045259' /scratch/stefan/7916127/working/building/REAL250005045259 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045259 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045259/0 /scratch/stefan/7916127/working/building/REAL250005045259 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/381 `/scratch/stefan/7916127/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=NS1)C1=CC(=O)[N-]O1) `REAL250005045259.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045259 none O=C(NCCNC(=O)C1=CN=NS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 30, 45, 87, 87, 87, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 11, 30, 30, 45, 45, 87, 117, 1] 117 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045259 none O=C(NCCNC(=O)C1=CN=NS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 8, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 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: [109, 109, 65, 43, 10, 11, 1, 11, 1, 1, 1, 1, 1, 109, 117, 117, 117, 117, 117, 109, 65, 65, 43, 43, 11, 1, 117] 117 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045259 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045259 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045259/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045259 Building REAL250005045260 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045260' /scratch/stefan/7916127/working/building/REAL250005045260 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045260 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045260/0 /scratch/stefan/7916127/working/building/REAL250005045260 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/382 `/scratch/stefan/7916127/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045260.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045260 none COC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 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] 0 hydrogens need rotated 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, 201, 109, 69, 69, 69, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 169, 109, 109, 69, 25, 25, 16, 16, 4, 1] 201 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]) total number of confs: 770 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045260 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045260 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045260/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045260 Building REAL250005045261 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045261' /scratch/stefan/7916127/working/building/REAL250005045261 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045261 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045261/0 /scratch/stefan/7916127/working/building/REAL250005045261 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/383 `/scratch/stefan/7916127/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NOC=C1) `REAL250005045261.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045261 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NOC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [7, 1, 7, 7, 23, 36, 66, 66, 66, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 7, 23, 23, 36, 36, 66, 72, 1, 1] 72 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) 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: REAL250005045261 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NOC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [66, 66, 38, 25, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 66, 72, 72, 72, 72, 66, 38, 38, 25, 25, 9, 1, 72, 72] 72 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045261 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045261 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045261/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045261 Building REAL250005045262 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045262' /scratch/stefan/7916127/working/building/REAL250005045262 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045262 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045262/0 /scratch/stefan/7916127/working/building/REAL250005045262 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/384 `/scratch/stefan/7916127/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045262.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045262 none CCCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 125, 79, 41, 41, 41, 19, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 79, 79, 41, 19, 19, 10, 10, 2, 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: 828 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045262 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045262 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045262/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045262 Building REAL250005045263 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045263' /scratch/stefan/7916127/working/building/REAL250005045263 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045263 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045263/0 /scratch/stefan/7916127/working/building/REAL250005045263 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/385 `/scratch/stefan/7916127/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045263.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045263 none CC(=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', '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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 8, 38, 38, 38, 103, 123, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 8, 8, 8, 8, 38, 103, 103, 123, 123, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045263 none CC(=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', '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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 75, 75, 75, 34, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 119, 201, 201, 119, 119, 119, 119, 75, 34, 34, 24, 24, 4, 1, 201, 201, 201, 201, 201] 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, 35]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045263 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045263 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045263/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045263 Building REAL250005045264 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045264' /scratch/stefan/7916127/working/building/REAL250005045264 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045264 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045264/0 /scratch/stefan/7916127/working/building/REAL250005045264 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/386 `/scratch/stefan/7916127/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045264.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045264 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 71, 71, 71, 33, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 71, 33, 33, 24, 24, 11, 1, 89] 89 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]) total number of confs: 266 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045264 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 31, 48, 81, 81, 81, 89, 89, 89, 89, 89, 1, 2, 2, 2, 1, 7, 31, 31, 48, 48, 81, 89, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045264 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045264 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045264/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045264 Building REAL250005045265 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045265' /scratch/stefan/7916127/working/building/REAL250005045265 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045265 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045265/0 /scratch/stefan/7916127/working/building/REAL250005045265 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/387 `/scratch/stefan/7916127/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1) `REAL250005045265.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045265 none O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [7, 1, 7, 7, 22, 37, 75, 75, 75, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 7, 22, 22, 37, 37, 75, 107, 107, 1] 107 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045265 none O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [103, 103, 60, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 103, 107, 107, 107, 107, 107, 103, 60, 60, 42, 42, 12, 1, 1, 107] 107 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045265 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045265 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045265/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045265 Building REAL250005045266 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045266' /scratch/stefan/7916127/working/building/REAL250005045266 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045266 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045266/0 /scratch/stefan/7916127/working/building/REAL250005045266 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/388 `/scratch/stefan/7916127/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045266.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045266 none CC1=NN(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 184, 131, 131, 131, 59, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 184, 131, 59, 59, 39, 39, 11, 1, 184] 184 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]) total number of confs: 513 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045266 none CC1=NN(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 97, 173, 173, 173, 184, 184, 184, 184, 184, 1, 2, 2, 2, 2, 2, 2, 10, 52, 52, 97, 97, 173, 184, 1] 184 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 679 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045266 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045266 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045266/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045266 Building REAL250005045267 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045267' /scratch/stefan/7916127/working/building/REAL250005045267 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045267 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045267/0 /scratch/stefan/7916127/working/building/REAL250005045267 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/389 `/scratch/stefan/7916127/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=C1) `REAL250005045267.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045267 none CC1=CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 101, 101, 101, 36, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 179, 179, 101, 36, 36, 20, 20, 4, 1, 201] 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]) total number of confs: 704 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045267 none CC1=CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 31, 31, 31, 85, 129, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 8, 8, 31, 85, 85, 129, 129, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045267 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045267 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045267/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045267 Building REAL250005045268 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045268' /scratch/stefan/7916127/working/building/REAL250005045268 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045268 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045268/0 /scratch/stefan/7916127/working/building/REAL250005045268 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/390 `/scratch/stefan/7916127/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)COC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045268.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045268 none CC(C)COC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 201, 139, 116, 62, 116, 62, 62, 22, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 163, 163, 116, 116, 116, 116, 62, 22, 22, 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: 873 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045268 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045268 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045268/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045268 Building REAL250005045269 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045269' /scratch/stefan/7916127/working/building/REAL250005045269 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045269 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045269/0 /scratch/stefan/7916127/working/building/REAL250005045269 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/391 `/scratch/stefan/7916127/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045269.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045269 none CCCC(=O)NCC(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 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] 0 hydrogens 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, 195, 123, 123, 133, 121, 60, 60, 60, 22, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 199, 199, 199, 199, 199, 195, 195, 133, 121, 121, 60, 22, 22, 13, 13, 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: 988 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045269 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045269 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045269/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045269 Building REAL250005045270 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045270' /scratch/stefan/7916127/working/building/REAL250005045270 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045270 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045270/0 /scratch/stefan/7916127/working/building/REAL250005045270 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/392 `/scratch/stefan/7916127/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045270.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045270 none CCC=C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 197, 70, 197, 70, 70, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 197, 197, 70, 23, 23, 14, 14, 4, 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: 601 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045270 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045270 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045270/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045270 Building REAL250005045271 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045271' /scratch/stefan/7916127/working/building/REAL250005045271 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045271 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045271/0 /scratch/stefan/7916127/working/building/REAL250005045271 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/393 `/scratch/stefan/7916127/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS(=O)(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045271.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045271 none CS(=O)(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.o2', 'O.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 6, 4, 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 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [150, 131, 150, 150, 83, 83, 83, 37, 29, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 150, 150, 150, 131, 131, 83, 37, 37, 29, 29, 10, 1] 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]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045271 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045271 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045271/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045271 Building REAL250005045272 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045272' /scratch/stefan/7916127/working/building/REAL250005045272 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045272 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045272/0 /scratch/stefan/7916127/working/building/REAL250005045272 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/394 `/scratch/stefan/7916127/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=C1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045272.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045272 none O=C(C=C1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 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, 6, 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, 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: [111, 111, 111, 155, 155, 155, 155, 155, 155, 50, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 111, 50, 50, 29, 29, 8, 1] 155 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: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045272 none O=C(C=C1CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 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, 6, 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, 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: [7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 40, 72, 146, 146, 146, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 40, 40, 72, 72, 146, 155] 155 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 32, 34, 35, 36, 37, 38, 33, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20]) total number of confs: 541 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045272 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045272 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045272/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045272 Building REAL250005045273 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045273' /scratch/stefan/7916127/working/building/REAL250005045273 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045273 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045273/0 /scratch/stefan/7916127/working/building/REAL250005045273 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/395 `/scratch/stefan/7916127/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=CO1) `REAL250005045273.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045273 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=CO1 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', 'N.2', 'C.2', 'O.3', '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, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 110, 110, 112, 52, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 112, 52, 52, 33, 33, 9, 1, 132] 132 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]) 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: REAL250005045273 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=CO1 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', 'N.2', 'C.2', 'O.3', '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, 8, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 34, 62, 126, 126, 126, 132, 132, 132, 132, 132, 1, 1, 1, 2, 2, 2, 7, 34, 34, 62, 62, 126, 132, 1] 132 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 490 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045273 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045273 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045273/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045273 Building REAL250005045274 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045274' /scratch/stefan/7916127/working/building/REAL250005045274 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045274 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045274/0 /scratch/stefan/7916127/working/building/REAL250005045274 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/396 `/scratch/stefan/7916127/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045274.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045274 none CCOC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 158, 149, 97, 149, 185, 97, 97, 34, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 149, 197, 197, 197, 197, 197, 97, 34, 34, 22, 22, 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: 929 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045274 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045274 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045274/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045274 Building REAL250005045275 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045275' /scratch/stefan/7916127/working/building/REAL250005045275 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045275 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045275/0 /scratch/stefan/7916127/working/building/REAL250005045275 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/397 `/scratch/stefan/7916127/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045275.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045275 none O=C(CC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 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: [114, 114, 114, 196, 197, 196, 197, 54, 34, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 197, 197, 114, 54, 54, 34, 34, 12, 1] 197 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]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045275 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045275 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045275/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045275 Building REAL250005045276 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045276' /scratch/stefan/7916127/working/building/REAL250005045276 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045276 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045276/0 /scratch/stefan/7916127/working/building/REAL250005045276 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/398 `/scratch/stefan/7916127/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045276.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045276 none COC(C)C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [199, 194, 132, 197, 132, 133, 55, 34, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 199, 199, 199, 197, 197, 197, 197, 133, 55, 55, 34, 34, 9, 1] 199 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]) total number of confs: 781 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045276 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045276 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045276/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045276 Building REAL250005045277 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045277' /scratch/stefan/7916127/working/building/REAL250005045277 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045277 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045277/0 /scratch/stefan/7916127/working/building/REAL250005045277 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/399 `/scratch/stefan/7916127/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045277.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045277 none CC(C)OCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 201, 147, 85, 85, 85, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 147, 147, 85, 27, 27, 16, 16, 4, 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: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045277 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045277 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045277/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045277 Building REAL250005045278 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045278' /scratch/stefan/7916127/working/building/REAL250005045278 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045278 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045278/0 /scratch/stefan/7916127/working/building/REAL250005045278 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/400 `/scratch/stefan/7916127/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(OCC1CC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045278.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045278 none CC(OCC1CC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 41, 64, 81, 124, 201, 201, 41, 41, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 124, 124, 201, 201, 201, 201, 201, 41, 18, 18, 10, 10, 2, 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: 799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045278 none CC(OCC1CC1)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 27, 10, 1, 1, 1, 1, 44, 77, 77, 77, 139, 146, 201, 201, 201, 201, 201, 201, 201, 201, 44, 44, 44, 44, 10, 10, 1, 1, 1, 1, 1, 77, 139, 139, 146, 146, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 27, 28, 29, 30, 31] set([0, 1, 2, 7, 8, 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: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045278 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045278 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045278/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045278 Building REAL250005045279 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045279' /scratch/stefan/7916127/working/building/REAL250005045279 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045279 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045279/0 /scratch/stefan/7916127/working/building/REAL250005045279 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/401 `/scratch/stefan/7916127/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045279.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045279 none CCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need 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, 121, 83, 45, 45, 45, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 147, 147, 83, 83, 45, 19, 19, 12, 12, 4, 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: 838 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045279 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045279 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045279/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045279 Building REAL250005045280 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045280' /scratch/stefan/7916127/working/building/REAL250005045280 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045280 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045280/0 /scratch/stefan/7916127/working/building/REAL250005045280 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/402 `/scratch/stefan/7916127/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045280.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045280 none CCCCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 106, 90, 84, 51, 84, 51, 51, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 106, 106, 84, 84, 84, 84, 51, 19, 19, 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: 914 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045280 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045280 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045280/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045280 Building REAL250005045281 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045281' /scratch/stefan/7916127/working/building/REAL250005045281 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045281 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045281/0 /scratch/stefan/7916127/working/building/REAL250005045281 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/403 `/scratch/stefan/7916127/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045281.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045281 none C=CCCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'O.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', '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, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 85, 78, 42, 78, 42, 42, 18, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 132, 132, 78, 78, 78, 78, 42, 18, 18, 11, 11, 3, 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: 956 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045281 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045281 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045281/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045281 Building REAL250005045282 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045282' /scratch/stefan/7916127/working/building/REAL250005045282 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045282 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045282/0 /scratch/stefan/7916127/working/building/REAL250005045282 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/404 `/scratch/stefan/7916127/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCOC1)C1=CC(=O)[N-]O1) `REAL250005045282.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045282 none O=C(NCCNC(=O)C1CCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 35, 54, 135, 135, 135, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 35, 35, 54, 54, 135, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 642 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: REAL250005045282 none O=C(NCCNC(=O)C1CCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 105, 61, 11, 11, 1, 11, 1, 1, 1, 1, 1, 190, 201, 201, 201, 201, 201, 190, 105, 105, 61, 61, 11, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 731 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045282 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045282 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045282/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045282 Building REAL250005045283 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045283' /scratch/stefan/7916127/working/building/REAL250005045283 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045283 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045283/0 /scratch/stefan/7916127/working/building/REAL250005045283 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/405 `/scratch/stefan/7916127/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=NC(F)=C1)C1=CC(=O)[N-]O1) `REAL250005045283.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045283 none O=C(NCCNC(=O)C1=CC=NC(F)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 32, 45, 85, 85, 85, 149, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 13, 32, 32, 45, 45, 85, 149, 149, 149, 1] 149 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045283 none O=C(NCCNC(=O)C1=CC=NC(F)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 149 conformations in input total number of sets (complete confs): 149 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 69, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 137, 149, 149, 149, 149, 149, 137, 69, 69, 37, 37, 7, 1, 1, 1, 149] 149 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 515 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045283 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045283 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045283/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045283 Building REAL250005045284 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045284' /scratch/stefan/7916127/working/building/REAL250005045284 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045284 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045284/0 /scratch/stefan/7916127/working/building/REAL250005045284 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/406 `/scratch/stefan/7916127/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1) `REAL250005045284.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045284 none CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 80, 80, 80, 39, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 80, 39, 39, 26, 26, 9, 1] 110 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]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045284 none CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 40, 57, 104, 104, 104, 110, 110, 110, 110, 110, 1, 2, 2, 2, 1, 8, 40, 40, 57, 57, 104, 110] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 383 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045284 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045284 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045284/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045284 Building REAL250005045285 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045285' /scratch/stefan/7916127/working/building/REAL250005045285 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045285 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045285/0 /scratch/stefan/7916127/working/building/REAL250005045285 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/407 `/scratch/stefan/7916127/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045285.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045285 none CN1N=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 83, 83, 83, 45, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 83, 45, 45, 30, 30, 11, 1] 107 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]) 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: REAL250005045285 none CN1N=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 51, 103, 103, 103, 107, 107, 107, 107, 107, 2, 2, 2, 1, 1, 10, 36, 36, 51, 51, 103, 107] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 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/7916127/working/building/REAL250005045285 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045285 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045285/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045285 Building REAL250005045286 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045286' /scratch/stefan/7916127/working/building/REAL250005045286 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045286 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045286/0 /scratch/stefan/7916127/working/building/REAL250005045286 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/408 `/scratch/stefan/7916127/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045286.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045286 none CCC(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens 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, 155, 101, 155, 161, 101, 101, 32, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 156, 161, 161, 161, 101, 32, 32, 18, 18, 4, 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: 931 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045286 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045286 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045286/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045286 Building REAL250005045287 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045287' /scratch/stefan/7916127/working/building/REAL250005045287 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045287 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045287/0 /scratch/stefan/7916127/working/building/REAL250005045287 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/409 `/scratch/stefan/7916127/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045287.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045287 none COCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 115, 110, 98, 29, 29, 29, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 115, 115, 114, 114, 98, 98, 29, 23, 23, 14, 14, 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: 952 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045287 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045287 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045287/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045287 Building REAL250005045288 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045288' /scratch/stefan/7916127/working/building/REAL250005045288 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045288 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045288/0 /scratch/stefan/7916127/working/building/REAL250005045288 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/410 `/scratch/stefan/7916127/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045288.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045288 none CCCC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 179, 119, 176, 25, 25, 25, 23, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 200, 200, 180, 180, 180, 180, 119, 119, 25, 23, 23, 15, 15, 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: 902 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045288 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045288 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045288/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045288 Building REAL250005045289 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045289' /scratch/stefan/7916127/working/building/REAL250005045289 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045289 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045289/0 /scratch/stefan/7916127/working/building/REAL250005045289 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/411 `/scratch/stefan/7916127/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045289.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045289 none COC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 161, 201, 86, 86, 86, 31, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 161, 161, 86, 31, 31, 22, 22, 4, 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: 844 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045289 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045289 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045289/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045289 Building REAL250005045290 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045290' /scratch/stefan/7916127/working/building/REAL250005045290 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045290 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045290/0 /scratch/stefan/7916127/working/building/REAL250005045290 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/412 `/scratch/stefan/7916127/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1) `REAL250005045290.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045290 none CN1C=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 132, 73, 73, 73, 25, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 132, 132, 73, 25, 25, 20, 20, 6, 1, 201] 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]) 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: REAL250005045290 none CN1C=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 21, 21, 21, 90, 106, 198, 198, 198, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 7, 7, 21, 90, 90, 106, 106, 198, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045290 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045290 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045290/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045290 Building REAL250005045291 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045291' /scratch/stefan/7916127/working/building/REAL250005045291 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045291 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045291/0 /scratch/stefan/7916127/working/building/REAL250005045291 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/413 `/scratch/stefan/7916127/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCCCC1)C1=CC(=O)[N-]O1) `REAL250005045291.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045291 none O=C(NCCNC(=O)C1CCCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 28, 46, 118, 118, 118, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 28, 28, 46, 46, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 40, 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, 38, 39]) total number of confs: 659 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: REAL250005045291 none O=C(NCCNC(=O)C1CCCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 100, 58, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 100, 100, 58, 58, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 38, 8, 9, 10, 11, 12, 13, 14, 39, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 725 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045291 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045291 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045291/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045291 Building REAL250005045292 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045292' /scratch/stefan/7916127/working/building/REAL250005045292 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045292 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045292/0 /scratch/stefan/7916127/working/building/REAL250005045292 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/414 `/scratch/stefan/7916127/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045292.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045292 none C=CCCC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 177, 79, 79, 79, 35, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 79, 35, 35, 20, 20, 4, 1] 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]) total number of confs: 849 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045292 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045292 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045292/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045292 Building REAL250005045293 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045293' /scratch/stefan/7916127/working/building/REAL250005045293 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045293 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045293/0 /scratch/stefan/7916127/working/building/REAL250005045293 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/415 `/scratch/stefan/7916127/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=COCCC1)C1=CC(=O)[N-]O1) `REAL250005045293.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045293 none O=C(NCCNC(=O)C1=COCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 32, 44, 94, 94, 94, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 8, 32, 32, 44, 44, 94, 178, 178, 178, 178, 178, 178, 178, 1] 178 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 445 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045293 none O=C(NCCNC(=O)C1=COCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 93, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 175, 178, 178, 178, 178, 178, 175, 93, 93, 61, 61, 12, 1, 1, 1, 1, 1, 1, 1, 178] 178 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045293 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045293 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045293/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045293 Building REAL250005045294 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045294' /scratch/stefan/7916127/working/building/REAL250005045294 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045294 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045294/0 /scratch/stefan/7916127/working/building/REAL250005045294 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/416 `/scratch/stefan/7916127/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045294.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045294 none COC(=O)C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 201, 132, 132, 53, 53, 53, 22, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 132, 132, 132, 132, 53, 22, 22, 14, 14, 4, 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: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045294 none COC(=O)C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 1, 4, 1, 1, 1, 1, 12, 12, 12, 56, 69, 129, 130, 129, 132, 132, 132, 132, 132, 4, 4, 4, 1, 1, 1, 1, 12, 56, 56, 69, 69, 130, 132] 201 rigid atoms, others: [2, 4, 5, 6, 7, 24, 25, 26, 27] set([0, 1, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045294 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045294 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045294/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045294 Building REAL250005045295 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045295' /scratch/stefan/7916127/working/building/REAL250005045295 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045295 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045295/0 /scratch/stefan/7916127/working/building/REAL250005045295 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/417 `/scratch/stefan/7916127/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCOC1)C1=CC(=O)[N-]O1) `REAL250005045295.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045295 none O=C(NCCNC(=O)C1CCCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 33, 49, 115, 115, 115, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 10, 33, 33, 49, 49, 115, 191, 191, 191, 191, 191, 191, 191, 191, 191, 1] 191 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045295 none O=C(NCCNC(=O)C1CCCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 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 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [181, 180, 108, 65, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 180, 191, 191, 191, 191, 191, 181, 108, 108, 65, 65, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 191] 191 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045295 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045295 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045295/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045295 Building REAL250005045296 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045296' /scratch/stefan/7916127/working/building/REAL250005045296 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045296 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045296/0 /scratch/stefan/7916127/working/building/REAL250005045296 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/418 `/scratch/stefan/7916127/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045296.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045296 none CCOCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need 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, 172, 155, 69, 69, 69, 33, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 172, 172, 155, 155, 69, 33, 33, 21, 21, 4, 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: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045296 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045296 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045296/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045296 Building REAL250005045297 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045297' /scratch/stefan/7916127/working/building/REAL250005045297 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045297 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045297/0 /scratch/stefan/7916127/working/building/REAL250005045297 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/419 `/scratch/stefan/7916127/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045297.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045297 none CCNC(=O)CCC(=O)NCCNC(=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.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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need 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, 125, 135, 121, 53, 53, 53, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 135, 125, 125, 121, 121, 53, 19, 19, 12, 12, 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: 954 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045297 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045297 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045297/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045297 Building REAL250005045298 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045298' /scratch/stefan/7916127/working/building/REAL250005045298 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045298 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045298/0 /scratch/stefan/7916127/working/building/REAL250005045298 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/420 `/scratch/stefan/7916127/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=N1) `REAL250005045298.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045298 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [4, 1, 4, 4, 23, 35, 67, 67, 67, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 4, 22, 22, 36, 36, 67, 73, 1, 1] 73 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) 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: REAL250005045298 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 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: [71, 71, 41, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 73, 73, 73, 73, 71, 41, 41, 28, 28, 9, 1, 73, 73] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045298 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045298 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045298/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045298 Building REAL250005045299 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045299' /scratch/stefan/7916127/working/building/REAL250005045299 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045299 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045299/0 /scratch/stefan/7916127/working/building/REAL250005045299 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/421 `/scratch/stefan/7916127/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045299.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045299 none COCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 88, 156, 88, 88, 32, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 156, 156, 156, 156, 88, 32, 32, 20, 20, 4, 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: 881 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045299 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045299 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045299/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045299 Building REAL250005045300 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045300' /scratch/stefan/7916127/working/building/REAL250005045300 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045300 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045300/0 /scratch/stefan/7916127/working/building/REAL250005045300 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/422 `/scratch/stefan/7916127/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045300.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045300 none CC(C)(C)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 185, 201, 185, 171, 57, 57, 57, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 171, 171, 57, 23, 23, 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: 1032 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045300 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045300 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045300/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045300 Building REAL250005045301 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045301' /scratch/stefan/7916127/working/building/REAL250005045301 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045301 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045301/0 /scratch/stefan/7916127/working/building/REAL250005045301 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/423 `/scratch/stefan/7916127/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045301.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045301 none C=CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 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, 84, 44, 44, 44, 17, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 84, 84, 44, 17, 17, 12, 12, 4, 1] 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]) total number of confs: 782 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045301 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045301 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045301/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045301 Building REAL250005045302 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045302' /scratch/stefan/7916127/working/building/REAL250005045302 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045302 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045302/0 /scratch/stefan/7916127/working/building/REAL250005045302 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/424 `/scratch/stefan/7916127/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC=N1) `REAL250005045302.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045302 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [5, 1, 5, 5, 21, 34, 69, 69, 69, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 5, 21, 21, 34, 34, 69, 73, 1, 1] 73 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045302 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [71, 71, 43, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 73, 73, 73, 73, 71, 43, 43, 28, 28, 9, 1, 73, 73] 73 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045302 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045302 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045302/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045302 Building REAL250005045303 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045303' /scratch/stefan/7916127/working/building/REAL250005045303 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045303 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045303/0 /scratch/stefan/7916127/working/building/REAL250005045303 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/425 `/scratch/stefan/7916127/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1CCC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045303.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045303 none O=C(NCCNC(=O)[C@H]1CCC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 13, 37, 47, 124, 124, 124, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 13, 37, 37, 47, 47, 124, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 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]) total number of confs: 645 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: REAL250005045303 none O=C(NCCNC(=O)[C@H]1CCC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 185, 102, 73, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 189, 102, 102, 73, 73, 12, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 740 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045303 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045303 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045303/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045303 Building REAL250005045304 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045304' /scratch/stefan/7916127/working/building/REAL250005045304 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045304 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045304/0 /scratch/stefan/7916127/working/building/REAL250005045304 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/426 `/scratch/stefan/7916127/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045304.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045304 none O=C(CC1=CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 172, 201, 201, 201, 201, 201, 33, 23, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 172, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 33, 33, 23, 23, 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: 713 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045304 none O=C(CC1=CCCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 1, 41, 41, 114, 125, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 114, 114, 125, 125, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 718 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045304 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045304 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045304/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045304 Building REAL250005045305 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045305' /scratch/stefan/7916127/working/building/REAL250005045305 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045305 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045305/0 /scratch/stefan/7916127/working/building/REAL250005045305 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/427 `/scratch/stefan/7916127/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045305.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045305 none CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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, 91, 67, 67, 67, 33, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 67, 33, 33, 22, 22, 9, 1, 91] 91 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]) total number of confs: 272 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045305 none CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 91 conformations in input total number of sets (complete confs): 91 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 38, 53, 89, 89, 89, 91, 91, 91, 91, 91, 1, 2, 2, 2, 1, 8, 38, 38, 53, 53, 89, 91, 1] 91 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045305 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045305 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045305/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045305 Building REAL250005045306 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045306' /scratch/stefan/7916127/working/building/REAL250005045306 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045306 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045306/0 /scratch/stefan/7916127/working/building/REAL250005045306 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/428 `/scratch/stefan/7916127/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045306.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045306 none CSCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 131, 72, 131, 72, 72, 25, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 163, 163, 131, 131, 131, 131, 72, 25, 25, 15, 15, 4, 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: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045306 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045306 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045306/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045306 Building REAL250005045307 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045307' /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045307 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045307/0 /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/429 `/scratch/stefan/7916127/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045307.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045307 none C[N@@H+]1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 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, 1, 7, 7, 7, 7, 7, 7, 6, 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] 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, 8, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 7, 1] 9 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: 28 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045307 none C[N@@H+]1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 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, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 6, 6, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 6, 6, 6, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045307/1 /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/430 `/scratch/stefan/7916127/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045307.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045307 none C[N@H+]1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 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, 1, 7, 7, 7, 7, 7, 7, 6, 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] 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, 8, 8, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 7, 1] 9 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: 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: REAL250005045307 none C[N@H+]1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 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, 1, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 6, 6, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 6, 6, 6, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045307/2 /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/431 `/scratch/stefan/7916127/working/3D/431' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045307.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045307/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045307 none CN1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 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] 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, 111, 111, 101, 101, 101, 46, 31, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 101, 46, 46, 31, 31, 8, 1] 111 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: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045307 none CN1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 5, 5, 1, 11, 8, 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, 7, 7, 6, 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] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 62, 108, 108, 108, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 35, 35, 62, 62, 108, 111] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045307 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045307 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045307/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045307/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045307/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045307 Building REAL250005045308 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045308' /scratch/stefan/7916127/working/building/REAL250005045308 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045308 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045308/0 /scratch/stefan/7916127/working/building/REAL250005045308 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/432 `/scratch/stefan/7916127/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045308.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045308 none CCC(=O)NCC(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 6, 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] 0 hydrogens need 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, 91, 60, 60, 60, 20, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 148, 91, 91, 60, 20, 20, 16, 16, 4, 1] 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]) total number of confs: 859 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045308 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045308 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045308/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045308 Building REAL250005045309 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045309' /scratch/stefan/7916127/working/building/REAL250005045309 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045309 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045309/0 /scratch/stefan/7916127/working/building/REAL250005045309 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/433 `/scratch/stefan/7916127/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045309.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045309 none CC(C)(C)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 201, 201, 195, 115, 115, 115, 43, 30, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 115, 43, 43, 30, 30, 9, 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: 673 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045309 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045309 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045309/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045309 Building REAL250005045310 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045310' /scratch/stefan/7916127/working/building/REAL250005045310 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045310 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045310/0 /scratch/stefan/7916127/working/building/REAL250005045310 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/434 `/scratch/stefan/7916127/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=C(F)N=C1)C1=CC(=O)[N-]O1) `REAL250005045310.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045310 none O=C(NCCNC(=O)C1=CC=C(F)N=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 33, 47, 86, 86, 86, 112, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 11, 33, 33, 47, 47, 86, 112, 112, 112, 1] 112 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045310 none O=C(NCCNC(=O)C1=CC=C(F)N=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 53, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 106, 112, 112, 112, 112, 112, 106, 53, 53, 31, 31, 7, 1, 1, 1, 112] 112 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 391 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045310 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045310 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045310/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045310 Building REAL250005045311 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045311' /scratch/stefan/7916127/working/building/REAL250005045311 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045311 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045311/0 /scratch/stefan/7916127/working/building/REAL250005045311 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/435 `/scratch/stefan/7916127/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C#N)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045311.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045311 none CC(C#N)C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.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, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 104, 166, 166, 104, 104, 42, 28, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 104, 42, 42, 28, 28, 8, 1] 166 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]) total number of confs: 633 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045311 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045311 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045311/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045311 Building REAL250005045312 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045312' /scratch/stefan/7916127/working/building/REAL250005045312 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045312 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045312/0 /scratch/stefan/7916127/working/building/REAL250005045312 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/436 `/scratch/stefan/7916127/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045312.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045312 none COCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 159, 110, 98, 43, 43, 43, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 159, 159, 98, 98, 43, 19, 19, 12, 12, 4, 1] 201 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: 941 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045312 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045312 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045312/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045312 Building REAL250005045313 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045313' /scratch/stefan/7916127/working/building/REAL250005045313 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045313 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045313/0 /scratch/stefan/7916127/working/building/REAL250005045313 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/437 `/scratch/stefan/7916127/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045313.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045313 none CCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 166, 61, 166, 61, 61, 33, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 197, 197, 166, 166, 166, 166, 61, 33, 33, 22, 22, 4, 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: 883 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045313 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045313 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045313/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045313 Building REAL250005045314 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045314' /scratch/stefan/7916127/working/building/REAL250005045314 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045314 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045314/0 /scratch/stefan/7916127/working/building/REAL250005045314 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/438 `/scratch/stefan/7916127/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045314.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045314 none CC1=NN(C)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 124, 77, 77, 77, 36, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 124, 77, 36, 36, 24, 24, 11, 1] 124 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: 333 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: REAL250005045314 none CC1=NN(C)C=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 51, 72, 118, 118, 118, 124, 124, 124, 124, 124, 2, 2, 2, 2, 2, 2, 1, 11, 51, 51, 72, 72, 118, 124] 124 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 27] set([8, 9, 10, 11, 12, 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: 467 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045314 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045314 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045314/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045314 Building REAL250005045315 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045315' /scratch/stefan/7916127/working/building/REAL250005045315 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045315 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045315/0 /scratch/stefan/7916127/working/building/REAL250005045315 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/439 `/scratch/stefan/7916127/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045315.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045315 none CC(C)(C)C(=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', '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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 201, 117, 188, 117, 117, 47, 29, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 47, 47, 29, 29, 7, 1] 201 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: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045315 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045315 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045315/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045315 Building REAL250005045316 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045316' /scratch/stefan/7916127/working/building/REAL250005045316 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045316 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045316/0 /scratch/stefan/7916127/working/building/REAL250005045316 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/440 `/scratch/stefan/7916127/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2CCC1O2)C1=CC(=O)[N-]O1) `REAL250005045316.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045316 none O=C(NCCNC(=O)C1CC2CCC1O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 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: [9, 1, 9, 9, 31, 43, 96, 96, 96, 114, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 9, 31, 31, 43, 43, 96, 114, 114, 114, 114, 114, 114, 114, 114, 114, 1] 114 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: 383 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: REAL250005045316 none O=C(NCCNC(=O)C1CC2CCC1O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 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: [107, 107, 45, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 107, 114, 114, 114, 114, 114, 107, 45, 45, 25, 25, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 114] 114 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 381 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045316 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045316 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045316/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045316 Building REAL250005045317 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045317' /scratch/stefan/7916127/working/building/REAL250005045317 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045317 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045317/0 /scratch/stefan/7916127/working/building/REAL250005045317 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/441 `/scratch/stefan/7916127/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005045317.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045317 none CC1=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 177, 78, 78, 78, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 177, 177, 78, 25, 25, 14, 14, 4, 1] 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]) 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: REAL250005045317 none CC1=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 29, 29, 29, 82, 116, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 7, 7, 29, 82, 82, 116, 116, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 741 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045317 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045317 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045317/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045317 Building REAL250005045318 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045318' /scratch/stefan/7916127/working/building/REAL250005045318 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045318 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045318/0 /scratch/stefan/7916127/working/building/REAL250005045318 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/442 `/scratch/stefan/7916127/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1) `REAL250005045318.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045318 none CCN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 137, 137, 137, 76, 76, 76, 33, 23, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 137, 137, 201, 201, 201, 201, 201, 137, 76, 33, 33, 23, 23, 8, 1, 137] 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]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045318 none CCN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 5, 5, 5, 30, 50, 131, 131, 131, 137, 137, 137, 137, 137, 1, 1, 9, 9, 9, 9, 9, 1, 5, 30, 30, 50, 50, 131, 137, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 34, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 481 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045318 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045318 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045318/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045318 Building REAL250005045319 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045319' /scratch/stefan/7916127/working/building/REAL250005045319 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045319 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045319/0 /scratch/stefan/7916127/working/building/REAL250005045319 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/443 `/scratch/stefan/7916127/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045319.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045319 none NC1=NC=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 3, 7, 7, 3, 7, 7, 6, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 89, 89, 45, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 45, 45, 29, 29, 7, 1] 89 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]) 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: REAL250005045319 none NC1=NC=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 3, 7, 7, 3, 7, 7, 6, 4, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 26, 41, 85, 85, 85, 89, 89, 89, 89, 89, 2, 2, 1, 1, 5, 26, 26, 41, 41, 85, 89] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045319 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045319 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045319/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045319 Building REAL250005045320 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045320' /scratch/stefan/7916127/working/building/REAL250005045320 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045320 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045320/0 /scratch/stefan/7916127/working/building/REAL250005045320 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/444 `/scratch/stefan/7916127/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045320.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045320 none O=C(CCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 145, 159, 201, 201, 19, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 145, 145, 167, 167, 201, 201, 201, 201, 201, 47, 19, 19, 14, 14, 4, 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: 848 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045320 none O=C(CCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 7, 3, 1, 1, 1, 1, 35, 35, 133, 149, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 3, 3, 1, 1, 1, 1, 1, 35, 133, 133, 149, 149, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 23, 24, 25, 26, 27] set([0, 1, 2, 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: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045320 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045320 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045320/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045320 Building REAL250005045321 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045321' /scratch/stefan/7916127/working/building/REAL250005045321 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045321 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045321/0 /scratch/stefan/7916127/working/building/REAL250005045321 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/445 `/scratch/stefan/7916127/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1) `REAL250005045321.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045321 none CC1=C(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', '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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 91, 91, 91, 51, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 91, 51, 51, 31, 31, 7, 1, 94] 94 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]) total number of confs: 330 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045321 none CC1=C(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', '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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 31, 45, 90, 90, 90, 94, 94, 94, 94, 94, 1, 1, 2, 2, 2, 2, 2, 2, 6, 31, 31, 45, 45, 90, 94, 1] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 19, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 343 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045321 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045321/1 /scratch/stefan/7916127/working/building/REAL250005045321 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/446 `/scratch/stefan/7916127/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1C) `REAL250005045321.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045321 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 117, 117, 117, 45, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 117, 45, 45, 32, 32, 8, 1, 201, 201, 201] 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]) total number of confs: 510 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: REAL250005045321 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens 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, 11, 11, 11, 67, 107, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 11, 67, 67, 107, 107, 193, 201, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 740 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045321 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045321 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045321/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045321/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045321 Building REAL250005045322 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045322' /scratch/stefan/7916127/working/building/REAL250005045322 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045322 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045322/0 /scratch/stefan/7916127/working/building/REAL250005045322 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/447 `/scratch/stefan/7916127/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045322.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045322 none O=C(CC1CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 170, 201, 201, 201, 201, 201, 26, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 26, 26, 17, 17, 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: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045322 none O=C(CC1CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 113, 129, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 113, 113, 129, 129, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 707 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045322 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045322 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045322/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045322 Building REAL250005045323 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045323' /scratch/stefan/7916127/working/building/REAL250005045323 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045323 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045323/0 /scratch/stefan/7916127/working/building/REAL250005045323 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/448 `/scratch/stefan/7916127/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045323.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045323 none CCCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 122, 113, 97, 46, 46, 46, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 122, 122, 97, 97, 46, 19, 19, 12, 12, 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: 863 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045323 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045323 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045323/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045323 Building REAL250005045324 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045324' /scratch/stefan/7916127/working/building/REAL250005045324 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045324 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045324/0 /scratch/stefan/7916127/working/building/REAL250005045324 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/449 `/scratch/stefan/7916127/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045324.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045324 none O=C(CC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 159, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 71, 23, 23, 14, 14, 4, 1] 201 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]) total number of confs: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045324 none O=C(CC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 31, 31, 105, 131, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 31, 105, 105, 131, 131, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 772 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045324 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045324 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045324/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045324 Building REAL250005045325 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045325' /scratch/stefan/7916127/working/building/REAL250005045325 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045325 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045325/0 /scratch/stefan/7916127/working/building/REAL250005045325 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/450 `/scratch/stefan/7916127/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=CO1) `REAL250005045325.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045325 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'C.2', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 183, 145, 145, 145, 50, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 183, 183, 183, 201, 201, 201, 201, 201, 145, 50, 50, 24, 24, 4, 1, 183] 201 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]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045325 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=CO1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.2', 'C.2', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens 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, 5, 5, 5, 28, 52, 168, 168, 168, 183, 183, 183, 183, 183, 1, 1, 1, 6, 6, 6, 5, 5, 5, 28, 28, 52, 52, 168, 183, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045325 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045325 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045325/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045325 Building REAL250005045326 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045326' /scratch/stefan/7916127/working/building/REAL250005045326 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045326 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045326/0 /scratch/stefan/7916127/working/building/REAL250005045326 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/451 `/scratch/stefan/7916127/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045326.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045326 none O=C(CC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 162, 201, 201, 201, 201, 32, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 163, 163, 201, 201, 201, 201, 201, 201, 201, 55, 32, 32, 22, 22, 4, 1] 201 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: 789 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045326 none O=C(CC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 30, 30, 109, 136, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 30, 109, 109, 136, 136, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045326 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045326 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045326/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045326 Building REAL250005045327 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045327' /scratch/stefan/7916127/working/building/REAL250005045327 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045327 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045327/0 /scratch/stefan/7916127/working/building/REAL250005045327 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/452 `/scratch/stefan/7916127/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC=CC1)C1=CC(=O)[N-]O1) `REAL250005045327.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045327 none O=C(NCCNC(=O)C1CC=CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 36, 54, 114, 114, 114, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 36, 36, 54, 54, 114, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045327 none O=C(NCCNC(=O)C1CC=CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 184, 97, 57, 9, 9, 1, 9, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 186, 97, 97, 57, 57, 9, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045327 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045327 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045327/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045327 Building REAL250005045328 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045328' /scratch/stefan/7916127/working/building/REAL250005045328 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045328 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045328/0 /scratch/stefan/7916127/working/building/REAL250005045328 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/453 `/scratch/stefan/7916127/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045328.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045328 none O=C(CC1=NNC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 164, 201, 201, 201, 201, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 76, 33, 33, 20, 20, 4, 1] 201 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]) total number of confs: 690 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045328 none O=C(CC1=NNC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 39, 39, 99, 123, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 1, 39, 99, 99, 123, 123, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045328 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045328 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045328/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045328 Building REAL250005045329 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045329' /scratch/stefan/7916127/working/building/REAL250005045329 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045329 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045329/0 /scratch/stefan/7916127/working/building/REAL250005045329 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/454 `/scratch/stefan/7916127/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=NC=C1F)C1=CC(=O)[N-]O1) `REAL250005045329.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045329 none O=C(NCCNC(=O)C1=CC=NC=C1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 47, 109, 109, 109, 198, 198, 198, 198, 198, 198, 1, 1, 1, 1, 1, 1, 9, 30, 30, 47, 47, 109, 198, 198, 198, 1] 198 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045329 none O=C(NCCNC(=O)C1=CC=NC=C1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 119, 76, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 190, 198, 198, 198, 198, 198, 190, 119, 119, 76, 76, 12, 1, 1, 1, 198] 198 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045329 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045329 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045329/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045329 Building REAL250005045330 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045330' /scratch/stefan/7916127/working/building/REAL250005045330 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045330 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045330/0 /scratch/stefan/7916127/working/building/REAL250005045330 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/455 `/scratch/stefan/7916127/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=NN1C) `REAL250005045330.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045330 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=NN1C 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', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 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: [143, 143, 124, 124, 124, 61, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 143, 143, 143, 143, 143, 143, 143, 124, 61, 61, 34, 34, 9, 1, 143, 143, 143] 143 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]) total number of confs: 466 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045330 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=NN1C 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', 'N.2', 'N.2', 'N.pl3', 'C.3', '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, 8, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 9, 9, 9, 45, 76, 131, 131, 131, 143, 143, 143, 143, 143, 1, 1, 1, 1, 2, 2, 2, 9, 45, 45, 76, 76, 131, 143, 2, 2, 2] 143 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045330 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045330 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045330/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045330 Building REAL250005045331 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045331' /scratch/stefan/7916127/working/building/REAL250005045331 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045331 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045331/0 /scratch/stefan/7916127/working/building/REAL250005045331 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/456 `/scratch/stefan/7916127/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045331.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045331 none CC1=CC=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 125, 125, 125, 50, 32, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 125, 50, 50, 32, 32, 8, 1] 201 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]) total number of confs: 527 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045331 none CC1=CC=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 59, 104, 199, 199, 199, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 10, 59, 59, 104, 104, 199, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045331 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045331 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045331/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045331 Building REAL250005045332 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045332' /scratch/stefan/7916127/working/building/REAL250005045332 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045332 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045332/0 /scratch/stefan/7916127/working/building/REAL250005045332 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/457 `/scratch/stefan/7916127/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045332.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045332 none CC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 131, 131, 131, 73, 73, 73, 43, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 131, 131, 131, 131, 131, 131, 73, 43, 43, 30, 30, 9, 1, 131] 131 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]) total number of confs: 358 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045332 none CC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 33, 59, 125, 125, 125, 131, 131, 131, 131, 131, 1, 2, 2, 2, 1, 1, 7, 33, 33, 59, 59, 125, 131, 1] 131 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 20, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 477 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045332 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045332 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045332/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045332 Building REAL250005045333 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045333' /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045333 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045333/0 /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/458 `/scratch/stefan/7916127/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045333.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045333 none CN1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 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: [193, 193, 193, 193, 193, 139, 139, 139, 60, 37, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 193, 193, 193, 139, 60, 60, 37, 37, 9, 1, 193, 193] 193 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]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045333 none CN1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 64, 113, 184, 186, 186, 193, 193, 193, 193, 193, 1, 2, 2, 2, 1, 1, 1, 1, 1, 11, 64, 64, 113, 113, 186, 193, 1, 1] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25, 26, 27, 28, 37, 36] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045333/1 /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/459 `/scratch/stefan/7916127/working/3D/459' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045333.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045333/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045333 none C[N@@H+]1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 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] 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, 20, 20, 20, 18, 18, 18, 13, 13, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 13, 13, 13, 13, 7, 1, 20, 20] 20 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: 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: REAL250005045333 none C[N@@H+]1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 14, 15, 17, 17, 17, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 14, 14, 15, 15, 17, 20, 1, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045333/2 /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/460 `/scratch/stefan/7916127/working/3D/460' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045333.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045333/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045333 none C[N@H+]1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 17, 17, 17, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 12, 12, 12, 12, 6, 1, 18, 18] 18 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: 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: REAL250005045333 none C[N@H+]1CCOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 3, 7, 7, 6, 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] 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, 1, 1, 8, 8, 8, 13, 14, 15, 15, 15, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 14, 14, 15, 18, 1, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37] set([32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045333 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045333 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045333/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045333/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045333/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045333 Building REAL250005045334 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045334' /scratch/stefan/7916127/working/building/REAL250005045334 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045334 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045334/0 /scratch/stefan/7916127/working/building/REAL250005045334 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/461 `/scratch/stefan/7916127/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045334.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045334 none CC1=NC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 127, 127, 127, 53, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 127, 53, 53, 34, 34, 9, 1] 164 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]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045334 none CC1=NC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 10, 56, 91, 158, 158, 158, 164, 164, 164, 164, 164, 1, 2, 2, 2, 2, 2, 2, 10, 56, 56, 91, 91, 158, 164] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 626 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045334 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045334 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045334/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045334 Building REAL250005045335 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045335' /scratch/stefan/7916127/working/building/REAL250005045335 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045335 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045335/0 /scratch/stefan/7916127/working/building/REAL250005045335 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/462 `/scratch/stefan/7916127/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045335.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045335 none O=C(CCC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 186, 159, 201, 201, 201, 29, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 188, 188, 201, 201, 77, 29, 29, 18, 18, 4, 1] 201 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]) total number of confs: 1098 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045335 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045335 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045335/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045335 Building REAL250005045336 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045336' /scratch/stefan/7916127/working/building/REAL250005045336 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045336 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045336/0 /scratch/stefan/7916127/working/building/REAL250005045336 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/463 `/scratch/stefan/7916127/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045336.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045336 none C=CCOCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', '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', '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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 129, 73, 69, 70, 41, 41, 41, 17, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 71, 71, 73, 73, 73, 73, 41, 17, 17, 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: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045336 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045336 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045336/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045336 Building REAL250005045337 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045337' /scratch/stefan/7916127/working/building/REAL250005045337 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045337 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045337/0 /scratch/stefan/7916127/working/building/REAL250005045337 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/464 `/scratch/stefan/7916127/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045337.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045337 none O=C(CC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 167, 201, 201, 201, 40, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 167, 167, 201, 201, 201, 201, 201, 201, 201, 85, 40, 40, 23, 23, 4, 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: 828 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045337 none O=C(CC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 33, 33, 107, 141, 199, 201, 199, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 33, 107, 107, 141, 141, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 800 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045337 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045337 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045337/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045337 Building REAL250005045338 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045338' /scratch/stefan/7916127/working/building/REAL250005045338 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045338 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045338/0 /scratch/stefan/7916127/working/building/REAL250005045338 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/465 `/scratch/stefan/7916127/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045338.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045338 none O=C(NCCNC(=O)C1=CC=CC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 37, 87, 87, 87, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 8, 28, 28, 37, 37, 87, 147, 147, 147, 147, 1] 147 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 378 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045338 none O=C(NCCNC(=O)C1=CC=CC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 81, 54, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 141, 147, 147, 147, 147, 147, 141, 81, 81, 54, 54, 10, 1, 1, 1, 1, 147] 147 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045338 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045338 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045338/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045338 Building REAL250005045339 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045339' /scratch/stefan/7916127/working/building/REAL250005045339 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045339 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045339/0 /scratch/stefan/7916127/working/building/REAL250005045339 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/466 `/scratch/stefan/7916127/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1(C)C) `REAL250005045339.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045339 none CC1(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 98, 98, 98, 51, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 98, 51, 51, 34, 34, 11, 1, 135, 135, 135, 135, 135, 135] 135 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: 482 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: REAL250005045339 none CC1(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1(C)C NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 19, 41, 120, 122, 120, 135, 135, 135, 135, 135, 1, 1, 1, 2, 2, 2, 2, 2, 2, 1, 3, 19, 19, 41, 41, 122, 135, 1, 1, 1, 2, 2, 2] 135 rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 18, 19, 20, 36, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 453 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045339 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045339 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045339/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045339 Building REAL250005045340 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045340' /scratch/stefan/7916127/working/building/REAL250005045340 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045340 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045340/0 /scratch/stefan/7916127/working/building/REAL250005045340 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/467 `/scratch/stefan/7916127/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=N1) `REAL250005045340.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045340 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=N1 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', 'O.3', 'C.2', 'N.2', '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, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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, 125, 125, 127, 55, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 127, 55, 55, 32, 32, 9, 1, 159] 159 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]) 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: REAL250005045340 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=N1 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', 'O.3', 'C.2', 'N.2', '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, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [1, 1, 1, 1, 9, 9, 9, 49, 83, 151, 151, 151, 159, 159, 159, 159, 159, 1, 1, 1, 2, 2, 2, 9, 49, 49, 83, 83, 151, 159, 1] 159 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045340 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045340 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045340/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045340 Building REAL250005045341 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045341' /scratch/stefan/7916127/working/building/REAL250005045341 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045341 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045341/0 /scratch/stefan/7916127/working/building/REAL250005045341 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/468 `/scratch/stefan/7916127/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045341.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045341 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', '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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7] 0 hydrogens 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, 19, 19, 19, 84, 125, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 4, 4, 4, 4, 19, 84, 84, 125, 125, 195, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 16, 17, 18, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 772 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045341 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', '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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7] 0 hydrogens 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, 115, 115, 115, 49, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 200, 201, 201, 200, 200, 200, 200, 115, 49, 49, 30, 30, 7, 1, 201, 201, 201, 201, 201] 201 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]) total number of confs: 791 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045341 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045341 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045341/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045341 Building REAL250005045342 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045342' /scratch/stefan/7916127/working/building/REAL250005045342 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045342 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045342/0 /scratch/stefan/7916127/working/building/REAL250005045342 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/469 `/scratch/stefan/7916127/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1C2CCCC21)C1=CC(=O)[N-]O1) `REAL250005045342.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045342 none O=C(NCCNC(=O)C1C2CCCC21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 34, 51, 112, 112, 112, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 7, 34, 34, 51, 51, 112, 141, 141, 141, 141, 141, 141, 141, 141, 141, 1] 141 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 486 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045342 none O=C(NCCNC(=O)C1C2CCCC21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [131, 129, 47, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 129, 141, 141, 141, 141, 141, 131, 47, 47, 25, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 141] 141 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045342 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045342 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045342/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045342 Building REAL250005045343 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045343' /scratch/stefan/7916127/working/building/REAL250005045343 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045343 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045343/0 /scratch/stefan/7916127/working/building/REAL250005045343 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/470 `/scratch/stefan/7916127/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045343.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045343 none N#CC1=CNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 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 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, 111, 111, 87, 87, 87, 34, 23, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 111, 111, 111, 87, 34, 34, 23, 23, 9, 1, 111] 111 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 333 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045343 none N#CC1=CNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 4, 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 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, 10, 10, 10, 42, 60, 103, 103, 103, 111, 111, 111, 111, 111, 1, 1, 1, 10, 42, 42, 60, 60, 103, 111, 1] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 405 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045343 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045343 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045343/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045343 Building REAL250005045344 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045344' /scratch/stefan/7916127/working/building/REAL250005045344 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045344 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045344/0 /scratch/stefan/7916127/working/building/REAL250005045344 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/471 `/scratch/stefan/7916127/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045344.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045344 none CC1=CSC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 136, 136, 136, 54, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 136, 54, 54, 32, 32, 11, 1] 201 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]) 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: REAL250005045344 none CC1=CSC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 57, 102, 193, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 9, 57, 57, 102, 102, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045344 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045344 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045344/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045344 Building REAL250005045345 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045345' /scratch/stefan/7916127/working/building/REAL250005045345 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045345 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045345/0 /scratch/stefan/7916127/working/building/REAL250005045345 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/472 `/scratch/stefan/7916127/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045345.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045345 none O=C(CCC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 124, 122, 201, 201, 201, 23, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 125, 157, 157, 201, 201, 201, 201, 201, 201, 201, 34, 23, 23, 16, 16, 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: 944 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045345 none O=C(CCC1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7, 7, 7] 0 hydrogens 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, 13, 6, 1, 1, 1, 1, 1, 50, 50, 140, 166, 201, 201, 201, 201, 201, 201, 201, 201, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 50, 140, 140, 166, 166, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 819 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045345 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045345 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045345/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045345 Building REAL250005045346 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045346' /scratch/stefan/7916127/working/building/REAL250005045346 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045346 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045346/0 /scratch/stefan/7916127/working/building/REAL250005045346 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/473 `/scratch/stefan/7916127/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045346.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045346 none CC1=CC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [165, 165, 165, 165, 165, 135, 135, 135, 63, 38, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 165, 165, 165, 165, 165, 165, 165, 165, 135, 63, 63, 38, 38, 11, 1] 165 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: 507 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045346 none CC1=CC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 53, 89, 155, 157, 155, 165, 165, 165, 165, 165, 1, 2, 2, 2, 1, 2, 2, 2, 9, 53, 53, 89, 89, 157, 165] 165 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 607 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045346 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045346 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045346/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045346 Building REAL250005045347 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045347' /scratch/stefan/7916127/working/building/REAL250005045347 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045347 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045347/0 /scratch/stefan/7916127/working/building/REAL250005045347 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/474 `/scratch/stefan/7916127/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045347.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045347 none O=C(CCC1=NN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [55, 55, 55, 89, 97, 102, 102, 102, 102, 29, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 89, 89, 97, 97, 102, 102, 55, 29, 29, 21, 21, 7, 1] 102 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]) total number of confs: 399 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045347 none O=C(CCC1=NN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 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: [26, 10, 6, 1, 1, 1, 1, 1, 1, 26, 26, 55, 66, 96, 96, 96, 102, 102, 102, 102, 102, 10, 10, 6, 6, 1, 1, 26, 55, 55, 66, 66, 96, 102] 102 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045347 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045347/1 /scratch/stefan/7916127/working/building/REAL250005045347 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/475 `/scratch/stefan/7916127/working/3D/475' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045347.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045347 none O=C(CCC1=NNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [15, 15, 15, 39, 47, 79, 79, 79, 79, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 39, 39, 47, 47, 79, 79, 15, 9, 9, 7, 7, 2, 1] 79 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]) 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: REAL250005045347 none O=C(CCC1=NNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [39, 18, 8, 1, 1, 1, 1, 1, 1, 39, 39, 71, 77, 79, 79, 79, 79, 79, 79, 79, 79, 18, 18, 8, 8, 1, 1, 39, 71, 71, 77, 77, 79, 79] 79 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 329 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045347 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045347 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045347/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045347/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045347 Building REAL250005045348 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045348' /scratch/stefan/7916127/working/building/REAL250005045348 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045348 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045348/0 /scratch/stefan/7916127/working/building/REAL250005045348 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/476 `/scratch/stefan/7916127/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045348.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045348 none CC1=CC=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 129, 129, 129, 63, 42, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 147, 147, 147, 147, 147, 147, 129, 63, 63, 42, 42, 11, 1] 147 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]) total number of confs: 457 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045348 none CC1=CC=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 46, 83, 143, 143, 143, 147, 147, 147, 147, 147, 2, 2, 2, 1, 1, 1, 10, 46, 46, 83, 83, 143, 147] 147 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045348 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045348 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045348/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045348 Building REAL250005045349 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045349' /scratch/stefan/7916127/working/building/REAL250005045349 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045349 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045349/0 /scratch/stefan/7916127/working/building/REAL250005045349 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/477 `/scratch/stefan/7916127/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1) `REAL250005045349.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045349 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1 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.2', 'C.2', 'N.pl3', '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, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 123, 123, 123, 56, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 123, 56, 56, 34, 34, 9, 1, 201, 201, 201] 201 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: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045349 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1 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.2', 'C.2', 'N.pl3', '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, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 49, 95, 191, 191, 191, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 49, 49, 95, 95, 191, 201, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 717 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045349 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045349 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045349/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045349 Building REAL250005045350 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045350' /scratch/stefan/7916127/working/building/REAL250005045350 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045350 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045350/0 /scratch/stefan/7916127/working/building/REAL250005045350 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/478 `/scratch/stefan/7916127/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045350.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045350 none CC=C(C)C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 141, 201, 141, 141, 59, 37, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 141, 59, 59, 37, 37, 9, 1] 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]) total number of confs: 686 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045350 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045350 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045350/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045350 Building REAL250005045351 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045351' /scratch/stefan/7916127/working/building/REAL250005045351 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045351 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045351/0 /scratch/stefan/7916127/working/building/REAL250005045351 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/479 `/scratch/stefan/7916127/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045351.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045351 none O=C(CCC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 141, 160, 201, 201, 201, 201, 27, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 141, 141, 187, 187, 201, 201, 201, 201, 201, 201, 201, 46, 27, 27, 16, 16, 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: 959 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045351 none O=C(CCC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 9, 5, 1, 1, 1, 1, 1, 1, 39, 39, 128, 152, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 39, 128, 128, 152, 152, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 817 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045351 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045351 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045351/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045351 Building REAL250005045352 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045352' /scratch/stefan/7916127/working/building/REAL250005045352 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045352 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045352/0 /scratch/stefan/7916127/working/building/REAL250005045352 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/480 `/scratch/stefan/7916127/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=COC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045352.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045352 none O=C(CCC1=COC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 135, 151, 201, 201, 201, 201, 15, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 135, 135, 151, 151, 201, 201, 201, 43, 15, 15, 10, 10, 2, 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: 704 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045352 none O=C(CCC1=COC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 4, 1, 1, 1, 1, 1, 1, 42, 42, 128, 155, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 4, 4, 1, 1, 1, 42, 134, 134, 153, 153, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 797 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045352 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045352 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045352/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045352 Building REAL250005045353 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045353' /scratch/stefan/7916127/working/building/REAL250005045353 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045353 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045353/0 /scratch/stefan/7916127/working/building/REAL250005045353 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/481 `/scratch/stefan/7916127/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC(F)(F)C1)C1=CC(=O)[N-]O1) `REAL250005045353.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045353 none O=C(NCCNC(=O)C1CC(F)(F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 44, 121, 121, 121, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 30, 30, 44, 44, 121, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 633 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: REAL250005045353 none O=C(NCCNC(=O)C1CC(F)(F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 114, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 195, 114, 114, 69, 69, 13, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 750 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045353 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045353 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045353/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045353 Building REAL250005045354 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045354' /scratch/stefan/7916127/working/building/REAL250005045354 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045354 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045354/0 /scratch/stefan/7916127/working/building/REAL250005045354 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/482 `/scratch/stefan/7916127/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045354.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045354 none CC1CC(C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 109, 109, 109, 55, 36, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 197, 197, 197, 197, 109, 55, 55, 36, 36, 13, 1, 197, 197] 197 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: 648 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: REAL250005045354 none CC1CC(C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 13, 13, 13, 55, 94, 175, 177, 175, 197, 197, 197, 197, 197, 1, 2, 2, 2, 1, 1, 1, 1, 13, 55, 55, 94, 94, 177, 197, 1, 1] 197 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 18, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 706 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045354 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045354 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045354/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045354 Building REAL250005045355 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045355' /scratch/stefan/7916127/working/building/REAL250005045355 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045355 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045355/0 /scratch/stefan/7916127/working/building/REAL250005045355 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/483 `/scratch/stefan/7916127/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)=C1CCCC1) `REAL250005045355.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045355 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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.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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 60, 100, 195, 197, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 10, 60, 60, 100, 100, 197, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 16, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045355 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)=C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', '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.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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 118, 118, 118, 44, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 118, 44, 44, 26, 26, 6, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 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: 642 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045355 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045355 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045355/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045355 Building REAL250005045356 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045356' /scratch/stefan/7916127/working/building/REAL250005045356 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045356 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045356/0 /scratch/stefan/7916127/working/building/REAL250005045356 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/484 `/scratch/stefan/7916127/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCCO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045356.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045356 none O=C(CC1CCCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 161, 201, 201, 201, 201, 201, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 80, 30, 30, 19, 19, 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: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045356 none O=C(CC1CCCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 29, 29, 85, 116, 199, 201, 199, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 85, 85, 116, 116, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 763 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045356 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045356 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045356/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045356 Building REAL250005045357 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045357' /scratch/stefan/7916127/working/building/REAL250005045357 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045357 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045357/0 /scratch/stefan/7916127/working/building/REAL250005045357 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/485 `/scratch/stefan/7916127/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1) `REAL250005045357.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045357 none CC1=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 131, 58, 58, 58, 21, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 131, 131, 58, 21, 21, 12, 12, 4, 1, 201] 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]) 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: REAL250005045357 none CC1=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 27, 27, 27, 81, 113, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 8, 8, 27, 81, 81, 113, 113, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 34, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045357 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045357/1 /scratch/stefan/7916127/working/building/REAL250005045357 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/486 `/scratch/stefan/7916127/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045357.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045357 none CC1=NNC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 161, 70, 70, 70, 26, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 161, 161, 70, 26, 26, 16, 16, 4, 1, 201] 201 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]) total number of confs: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045357 none CC1=NNC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 98, 110, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 9, 9, 43, 98, 98, 110, 110, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045357 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045357 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045357/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045357/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045357 Building REAL250005045358 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045358' /scratch/stefan/7916127/working/building/REAL250005045358 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045358 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045358/0 /scratch/stefan/7916127/working/building/REAL250005045358 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/487 `/scratch/stefan/7916127/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=C1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045358.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045358 none O=C(C=C1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 201, 201, 201, 201, 54, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 124, 54, 54, 32, 32, 7, 1] 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]) total number of confs: 668 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: REAL250005045358 none O=C(C=C1CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 11, 11, 65, 110, 193, 194, 193, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 11, 65, 65, 110, 110, 194, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 23, 24, 25] set([0, 32, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31]) total number of confs: 753 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045358 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045358 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045358/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045358 Building REAL250005045359 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045359' /scratch/stefan/7916127/working/building/REAL250005045359 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045359 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045359/0 /scratch/stefan/7916127/working/building/REAL250005045359 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/488 `/scratch/stefan/7916127/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CC(F)=C1)C1=CC(=O)[N-]O1) `REAL250005045359.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045359 none O=C(NCCNC(=O)C1=CN=CC(F)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 46, 88, 88, 88, 162, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 1, 9, 32, 32, 46, 46, 88, 162, 162, 162, 1] 162 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 424 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045359 none O=C(NCCNC(=O)C1=CN=CC(F)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 68, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 151, 162, 162, 162, 162, 162, 151, 68, 68, 33, 33, 7, 1, 1, 1, 162] 162 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045359 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045359 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045359/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045359 Building REAL250005045360 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045360' /scratch/stefan/7916127/working/building/REAL250005045360 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045360 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045360/0 /scratch/stefan/7916127/working/building/REAL250005045360 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/489 `/scratch/stefan/7916127/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)CC) `REAL250005045360.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045360 none CCC(=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)CC NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 116, 116, 73, 73, 73, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 116, 160, 152, 152, 152, 152, 152, 116, 73, 25, 25, 16, 16, 4, 1, 160, 160, 160, 160, 160] 201 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: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045360 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045360 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045360/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045360 Building REAL250005045361 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045361' /scratch/stefan/7916127/working/building/REAL250005045361 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045361 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045361/0 /scratch/stefan/7916127/working/building/REAL250005045361 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/490 `/scratch/stefan/7916127/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)NC=C1)C1=CC(=O)[N-]O1) `REAL250005045361.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045361 none O=C(NCCNC(=O)C1=CC(=O)NC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 28, 41, 79, 79, 79, 143, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 11, 28, 28, 41, 41, 79, 140, 143, 143, 143, 1] 143 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 369 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045361 none O=C(NCCNC(=O)C1=CC(=O)NC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [137, 137, 67, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 137, 143, 143, 143, 143, 143, 137, 67, 67, 37, 37, 7, 1, 1, 1, 1, 143] 143 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 507 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045361 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045361 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045361/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045361 Building REAL250005045362 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045362' /scratch/stefan/7916127/working/building/REAL250005045362 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045362 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045362/0 /scratch/stefan/7916127/working/building/REAL250005045362 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/491 `/scratch/stefan/7916127/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045362.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045362 none CC(C)=C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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: [146, 146, 146, 119, 146, 119, 119, 53, 34, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 146, 146, 119, 53, 53, 34, 34, 10, 1] 146 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]) total number of confs: 517 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045362 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045362 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045362/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045362 Building REAL250005045363 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045363' /scratch/stefan/7916127/working/building/REAL250005045363 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045363 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045363/0 /scratch/stefan/7916127/working/building/REAL250005045363 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/492 `/scratch/stefan/7916127/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCNC(=O)C1)C1=CC(=O)[N-]O1) `REAL250005045363.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045363 none O=C(NCCNC(=O)C1CCNC(=O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [9, 1, 9, 9, 34, 50, 114, 114, 114, 191, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 9, 34, 34, 50, 50, 114, 191, 191, 191, 191, 191, 191, 191, 191, 1] 191 rigid atoms, others: [1, 35, 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]) total number of confs: 634 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: REAL250005045363 none O=C(NCCNC(=O)C1CCNC(=O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [183, 182, 103, 64, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 182, 191, 191, 191, 191, 191, 183, 103, 103, 64, 64, 12, 1, 1, 1, 1, 1, 1, 1, 1, 191] 191 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 712 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045363 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045363 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045363/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045363 Building REAL250005045364 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045364' /scratch/stefan/7916127/working/building/REAL250005045364 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045364 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045364/0 /scratch/stefan/7916127/working/building/REAL250005045364 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/493 `/scratch/stefan/7916127/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCCC1) `REAL250005045364.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045364 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [11, 1, 11, 11, 42, 64, 96, 96, 96, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 11, 42, 42, 64, 64, 96, 103, 1, 1, 1, 1, 1, 1, 1] 103 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045364 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [102, 100, 52, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 100, 103, 103, 103, 103, 102, 52, 52, 35, 35, 11, 1, 103, 103, 103, 103, 103, 103, 103] 103 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045364 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045364 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045364/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045364 Building REAL250005045365 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045365' /scratch/stefan/7916127/working/building/REAL250005045365 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045365 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045365/0 /scratch/stefan/7916127/working/building/REAL250005045365 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/494 `/scratch/stefan/7916127/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=C1CCCC1) `REAL250005045365.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045365 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 60, 106, 196, 198, 196, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 9, 60, 60, 106, 106, 198, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) 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: REAL250005045365 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(F)=C1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'F', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 15, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7] 0 hydrogens 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, 44, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 124, 44, 44, 26, 26, 6, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 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, 34, 35]) total number of confs: 643 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045365 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045365 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045365/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045365 Building REAL250005045366 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045366' /scratch/stefan/7916127/working/building/REAL250005045366 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045366 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045366/0 /scratch/stefan/7916127/working/building/REAL250005045366 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/495 `/scratch/stefan/7916127/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045366.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045366 none CN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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: [154, 154, 154, 154, 101, 101, 101, 56, 38, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 101, 56, 56, 38, 38, 11, 1, 154] 154 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]) total number of confs: 459 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045366 none CN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 5, 5, 5, 30, 66, 139, 139, 139, 154, 154, 154, 154, 154, 1, 2, 2, 2, 1, 1, 5, 30, 30, 66, 66, 139, 154, 1] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045366 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045366 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045366/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045366 Building REAL250005045367 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045367' /scratch/stefan/7916127/working/building/REAL250005045367 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045367 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045367/0 /scratch/stefan/7916127/working/building/REAL250005045367 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/496 `/scratch/stefan/7916127/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045367.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045367 none CN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 69, 69, 69, 35, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 69, 35, 35, 22, 22, 7, 1, 71] 71 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]) 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: REAL250005045367 none CN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 35, 65, 65, 65, 71, 71, 71, 71, 71, 1, 2, 2, 2, 1, 5, 23, 23, 35, 35, 65, 71, 1] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045367 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045367 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045367/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045367 Building REAL250005045368 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045368' /scratch/stefan/7916127/working/building/REAL250005045368 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045368 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045368/0 /scratch/stefan/7916127/working/building/REAL250005045368 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/497 `/scratch/stefan/7916127/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1COC(=O)C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045368.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045368 none O=C(CC1COC(=O)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 184, 201, 201, 201, 201, 201, 34, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 184, 184, 201, 201, 201, 201, 201, 60, 34, 34, 22, 22, 4, 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: 783 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045368 none O=C(CC1COC(=O)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 7, 5, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 33, 33, 105, 125, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 33, 105, 105, 125, 125, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27] set([0, 1, 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: 711 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045368 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045368 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045368/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045368 Building REAL250005045369 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045369' /scratch/stefan/7916127/working/building/REAL250005045369 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045369 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045369/0 /scratch/stefan/7916127/working/building/REAL250005045369 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/498 `/scratch/stefan/7916127/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C)OC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045369.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045369 none CC1=C(C)OC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 77, 77, 77, 39, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 77, 39, 39, 22, 22, 7, 1, 89] 89 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]) 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: REAL250005045369 none CC1=C(C)OC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 45, 83, 83, 83, 89, 89, 89, 89, 89, 1, 2, 2, 2, 2, 2, 2, 7, 29, 29, 45, 45, 83, 89, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045369 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045369 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045369/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045369 Building REAL250005045370 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045370' /scratch/stefan/7916127/working/building/REAL250005045370 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045370 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045370/0 /scratch/stefan/7916127/working/building/REAL250005045370 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/499 `/scratch/stefan/7916127/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045370.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045370 none O=C(CC1=CC=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 125, 201, 201, 201, 201, 201, 21, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 63, 21, 21, 16, 16, 4, 1] 201 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]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045370 none O=C(CC1=CC=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 1, 1, 1, 1, 1, 1, 1, 17, 17, 94, 116, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 17, 94, 94, 116, 116, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045370 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045370 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045370/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045370 Building REAL250005045371 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045371' /scratch/stefan/7916127/working/building/REAL250005045371 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045371 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045371/0 /scratch/stefan/7916127/working/building/REAL250005045371 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/500 `/scratch/stefan/7916127/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCCO1)C1=CC(=O)[N-]O1) `REAL250005045371.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045371 none O=C(NCCNC(=O)C1CCCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 26, 36, 88, 88, 88, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 7, 26, 26, 36, 36, 88, 145, 145, 145, 145, 145, 145, 145, 145, 145, 1] 145 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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: REAL250005045371 none O=C(NCCNC(=O)C1CCCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 145 conformations in input total number of sets (complete confs): 145 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 92, 73, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 141, 145, 145, 145, 145, 145, 141, 92, 92, 73, 73, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 145] 145 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 527 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045371 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045371 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045371/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045371 Building REAL250005045372 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045372' /scratch/stefan/7916127/working/building/REAL250005045372 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045372 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045372/0 /scratch/stefan/7916127/working/building/REAL250005045372 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/501 `/scratch/stefan/7916127/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1=O) `REAL250005045372.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045372 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 119, 119, 119, 45, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 119, 45, 45, 29, 29, 9, 1] 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]) total number of confs: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045372 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 13, 13, 13, 77, 114, 197, 198, 197, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 13, 77, 77, 114, 114, 198, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045372 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045372 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045372/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045372 Building REAL250005045373 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045373' /scratch/stefan/7916127/working/building/REAL250005045373 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045373 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045373/0 /scratch/stefan/7916127/working/building/REAL250005045373 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/502 `/scratch/stefan/7916127/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(SC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045373.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045373 none CCC(SC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 130, 79, 131, 178, 79, 79, 29, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 163, 131, 178, 178, 178, 79, 29, 29, 17, 17, 4, 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: 807 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045373 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045373 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045373/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045373 Building REAL250005045374 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045374' /scratch/stefan/7916127/working/building/REAL250005045374 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045374 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045374/0 /scratch/stefan/7916127/working/building/REAL250005045374 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/503 `/scratch/stefan/7916127/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CC=C1) `REAL250005045374.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045374 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CC=C1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 42, 42, 42, 109, 130, 199, 199, 199, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 10, 10, 10, 10, 42, 109, 109, 130, 130, 199, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 745 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: REAL250005045374 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=CC=C1 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', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', '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, 8, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 102, 102, 102, 37, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 194, 201, 201, 201, 201, 193, 194, 194, 194, 102, 37, 37, 22, 22, 7, 1, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045374 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045374 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045374/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045374 Building REAL250005045375 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045375' /scratch/stefan/7916127/working/building/REAL250005045375 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045375 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045375/0 /scratch/stefan/7916127/working/building/REAL250005045375 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/504 `/scratch/stefan/7916127/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NC=N1) `REAL250005045375.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045375 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 87, 87, 87, 47, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 87, 47, 47, 32, 32, 7, 1, 89] 89 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]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045375 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 25, 41, 85, 85, 85, 89, 89, 89, 89, 89, 1, 1, 1, 2, 2, 2, 1, 5, 25, 25, 41, 41, 85, 89, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 315 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045375 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045375 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045375/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045375 Building REAL250005045376 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045376' /scratch/stefan/7916127/working/building/REAL250005045376 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045376 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045376/0 /scratch/stefan/7916127/working/building/REAL250005045376 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/505 `/scratch/stefan/7916127/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045376.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045376 none CC1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 129, 129, 129, 61, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 159, 159, 159, 129, 61, 61, 37, 37, 11, 1] 159 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: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045376 none CC1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 76, 146, 148, 148, 159, 159, 159, 159, 159, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 47, 47, 76, 76, 148, 159] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 25, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045376 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045376 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045376/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045376 Building REAL250005045377 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045377' /scratch/stefan/7916127/working/building/REAL250005045377 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045377 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045377/0 /scratch/stefan/7916127/working/building/REAL250005045377 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/506 `/scratch/stefan/7916127/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045377.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045377 none N#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 96, 96, 96, 46, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 120, 120, 120, 96, 46, 46, 34, 34, 11, 1, 120] 120 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30]) total number of confs: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045377 none N#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', 'C.2', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 43, 62, 112, 112, 112, 120, 120, 120, 120, 120, 1, 1, 1, 11, 42, 42, 62, 62, 112, 120, 1] 120 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 431 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045377 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045377 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045377/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045377 Building REAL250005045378 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045378' /scratch/stefan/7916127/working/building/REAL250005045378 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045378 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045378/0 /scratch/stefan/7916127/working/building/REAL250005045378 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/507 `/scratch/stefan/7916127/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)OCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045378.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045378 none CCC(C)OCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 167, 180, 114, 62, 62, 62, 22, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 180, 180, 114, 114, 62, 22, 22, 13, 13, 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: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045378 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045378 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045378/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045378 Building REAL250005045379 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045379' /scratch/stefan/7916127/working/building/REAL250005045379 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045379 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045379/0 /scratch/stefan/7916127/working/building/REAL250005045379 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/508 `/scratch/stefan/7916127/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045379.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045379 none CC1(C)C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [159, 159, 159, 159, 129, 159, 129, 129, 61, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 159, 159, 129, 61, 61, 37, 37, 11, 1] 159 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: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045379 none CC1(C)C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 76, 146, 148, 146, 159, 159, 159, 159, 159, 2, 2, 2, 2, 2, 2, 1, 1, 9, 47, 47, 76, 76, 148, 159] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27] set([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: 578 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045379 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045379 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045379/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045379 Building REAL250005045380 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045380' /scratch/stefan/7916127/working/building/REAL250005045380 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045380 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045380/0 /scratch/stefan/7916127/working/building/REAL250005045380 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/509 `/scratch/stefan/7916127/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045380.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045380 none CC1=CC=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 150, 57, 57, 57, 25, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 150, 150, 57, 25, 25, 16, 16, 4, 1] 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]) 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: REAL250005045380 none CC1=CC=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 44, 44, 44, 115, 133, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 7, 7, 44, 115, 115, 133, 133, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 767 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045380 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045380 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045380/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045380 Building REAL250005045381 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045381' /scratch/stefan/7916127/working/building/REAL250005045381 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045381 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045381/0 /scratch/stefan/7916127/working/building/REAL250005045381 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/510 `/scratch/stefan/7916127/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045381.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045381 none CC(O)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 6, 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, 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: [4, 1, 4, 4, 14, 32, 32, 32, 73, 82, 122, 122, 122, 122, 122, 122, 122, 122, 1, 1, 1, 5, 5, 5, 12, 14, 14, 32, 73, 73, 82, 82, 122, 122, 1, 1, 1, 1, 1] 366 rigid atoms, others: [1, 34, 35, 36, 37, 38, 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, 32, 33]) total number of confs: 484 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045381 none CC(O)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 6, 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, 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: [120, 85, 121, 44, 44, 44, 19, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 118, 122, 122, 121, 121, 121, 363, 85, 85, 44, 19, 19, 13, 13, 4, 1, 122, 122, 122, 122, 122] 366 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: 918 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045381 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045381 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045381/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045381 Building REAL250005045382 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045382' /scratch/stefan/7916127/working/building/REAL250005045382 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045382 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045382/0 /scratch/stefan/7916127/working/building/REAL250005045382 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/511 `/scratch/stefan/7916127/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCO1) `REAL250005045382.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045382 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCO1 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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 92, 92, 92, 43, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 129, 129, 129, 129, 129, 129, 129, 92, 43, 43, 24, 24, 7, 1, 129, 129, 129, 129, 129, 129] 129 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: 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: REAL250005045382 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCO1 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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 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 129 conformations in input total number of sets (complete confs): 129 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 30, 50, 117, 119, 119, 129, 129, 129, 129, 129, 1, 1, 1, 1, 2, 2, 2, 7, 30, 30, 50, 50, 119, 129, 1, 1, 1, 1, 1, 1] 129 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 442 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045382 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045382 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045382/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045382 Building REAL250005045383 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045383' /scratch/stefan/7916127/working/building/REAL250005045383 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045383 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045383/0 /scratch/stefan/7916127/working/building/REAL250005045383 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/512 `/scratch/stefan/7916127/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045383 none CSC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 135, 163, 63, 63, 63, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 163, 163, 163, 163, 135, 135, 63, 25, 25, 16, 16, 4, 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: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045383 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045383 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045383/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045383 Building REAL250005045384 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045384' /scratch/stefan/7916127/working/building/REAL250005045384 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045384 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045384/0 /scratch/stefan/7916127/working/building/REAL250005045384 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/513 `/scratch/stefan/7916127/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045384 none O=C(CN1CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 12, 5, 5, 8, 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: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 195, 201, 201, 201, 201, 201, 43, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 128, 43, 43, 26, 26, 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: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045384 none O=C(CN1CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 10, 5, 5, 12, 5, 5, 8, 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: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 19, 19, 72, 104, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 72, 72, 104, 104, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 735 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045384 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045384 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045384/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045384 Building REAL250005045385 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045385' /scratch/stefan/7916127/working/building/REAL250005045385 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045385 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045385/0 /scratch/stefan/7916127/working/building/REAL250005045385 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/514 `/scratch/stefan/7916127/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CCCO1)C1=CC(=O)[N-]O1) `REAL250005045385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045385 none O=C(NCCNC(=O)[C@@H]1CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 26, 36, 81, 81, 81, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 8, 26, 26, 36, 36, 81, 123, 123, 123, 123, 123, 123, 1] 123 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005045385 none O=C(NCCNC(=O)[C@@H]1CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [121, 120, 77, 59, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 120, 123, 123, 123, 123, 123, 121, 77, 77, 59, 59, 11, 1, 1, 1, 1, 1, 1, 123] 123 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045385 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045385 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045385/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045385 Building REAL250005045386 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045386' /scratch/stefan/7916127/working/building/REAL250005045386 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045386 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045386/0 /scratch/stefan/7916127/working/building/REAL250005045386 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/515 `/scratch/stefan/7916127/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=NC=N1) `REAL250005045386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045386 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=NC=N1 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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 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: [10, 1, 10, 31, 31, 31, 75, 81, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 10, 10, 10, 10, 31, 75, 75, 81, 81, 93, 93, 1, 1] 93 rigid atoms, others: [32, 1, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005045386 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N1C=NC=N1 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', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 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: [79, 47, 47, 47, 21, 16, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 79, 93, 93, 93, 93, 79, 79, 79, 79, 47, 21, 21, 16, 16, 5, 1, 93, 93] 93 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045386 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045386 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045386/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045386 Building REAL250005045387 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045387' /scratch/stefan/7916127/working/building/REAL250005045387 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045387 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045387/0 /scratch/stefan/7916127/working/building/REAL250005045387 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/516 `/scratch/stefan/7916127/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045387 none NC(=O)NC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 6, 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] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 168, 166, 121, 121, 121, 53, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 166, 166, 168, 168, 168, 121, 53, 53, 34, 34, 9, 1, 166, 166, 166, 166] 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, 34]) total number of confs: 555 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045387 none NC(=O)NC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 6, 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] 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: [3, 3, 3, 1, 1, 1, 12, 12, 12, 52, 83, 153, 153, 153, 166, 166, 166, 166, 166, 1, 1, 3, 3, 3, 12, 52, 52, 83, 83, 153, 166, 1, 1, 1, 1] 168 rigid atoms, others: [32, 33, 34, 3, 4, 5, 19, 20, 31] 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]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045387 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045387 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045387/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045387 Building REAL250005045388 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045388' /scratch/stefan/7916127/working/building/REAL250005045388 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045388 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045388/0 /scratch/stefan/7916127/working/building/REAL250005045388 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/517 `/scratch/stefan/7916127/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCOCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045388 none CN1CCOCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.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', '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, 12, 5, 5, 1, 11, 8, 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, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 132, 132, 105, 105, 105, 50, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 105, 50, 50, 34, 34, 9, 1] 132 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: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045388 none CN1CCOCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'O.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', '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, 12, 5, 5, 1, 11, 8, 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, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 37, 63, 124, 124, 124, 132, 132, 132, 132, 132, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 37, 37, 63, 63, 124, 132] 132 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045388 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045388 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045388/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045388 Building REAL250005045389 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045389' /scratch/stefan/7916127/working/building/REAL250005045389 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045389 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045389/0 /scratch/stefan/7916127/working/building/REAL250005045389 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/518 `/scratch/stefan/7916127/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NSC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045389 none CC1=NSC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [172, 170, 172, 172, 172, 106, 106, 106, 42, 26, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 106, 42, 42, 26, 26, 8, 1] 172 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]) total number of confs: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045389 none CC1=NSC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 58, 98, 166, 166, 166, 172, 172, 172, 172, 172, 2, 2, 2, 1, 9, 58, 58, 98, 98, 166, 172] 172 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 658 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045389 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045389 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045389/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045389 Building REAL250005045390 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045390' /scratch/stefan/7916127/working/building/REAL250005045390 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045390 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045390/0 /scratch/stefan/7916127/working/building/REAL250005045390 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/519 `/scratch/stefan/7916127/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045390 none C#CCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 142, 124, 39, 39, 39, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 147, 147, 147, 147, 125, 125, 39, 23, 23, 14, 14, 4, 1] 201 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: 942 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045390 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045390 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045390/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045390 Building REAL250005045391 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045391' /scratch/stefan/7916127/working/building/REAL250005045391 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045391 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045391/0 /scratch/stefan/7916127/working/building/REAL250005045391 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/520 `/scratch/stefan/7916127/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045391 none CC(C)(C)OCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 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: [172, 172, 172, 172, 169, 130, 130, 130, 53, 34, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 172, 130, 53, 53, 34, 34, 8, 1] 172 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: 670 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045391 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045391 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045391/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045391 Building REAL250005045392 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045392' /scratch/stefan/7916127/working/building/REAL250005045392 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045392 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045392/0 /scratch/stefan/7916127/working/building/REAL250005045392 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/521 `/scratch/stefan/7916127/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN1) `REAL250005045392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045392 none N#CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 81, 81, 81, 44, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 133, 133, 133, 81, 44, 44, 30, 30, 11, 1, 133, 133] 133 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30]) 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: REAL250005045392 none N#CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.2', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 31, 59, 123, 123, 123, 133, 133, 133, 133, 133, 1, 1, 1, 5, 31, 31, 59, 59, 123, 133, 1, 1] 133 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045392 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045392 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045392/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045392 Building REAL250005045393 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045393' /scratch/stefan/7916127/working/building/REAL250005045393 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045393 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045393/0 /scratch/stefan/7916127/working/building/REAL250005045393 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/522 `/scratch/stefan/7916127/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045393 none C#CCNC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 197, 197, 134, 197, 48, 48, 48, 20, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 134, 134, 48, 20, 20, 13, 13, 4, 1] 201 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]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045393 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045393 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045393/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045393 Building REAL250005045394 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045394' /scratch/stefan/7916127/working/building/REAL250005045394 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045394 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045394/0 /scratch/stefan/7916127/working/building/REAL250005045394 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/523 `/scratch/stefan/7916127/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045394 none CCNC(=O)CC(=O)NCCNC(=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', '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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 151, 151, 113, 151, 49, 49, 49, 19, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 151, 113, 113, 49, 19, 19, 16, 16, 4, 1] 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]) total number of confs: 889 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045394 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045394 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045394/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045394 Building REAL250005045395 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045395' /scratch/stefan/7916127/working/building/REAL250005045395 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045395 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045395/0 /scratch/stefan/7916127/working/building/REAL250005045395 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/524 `/scratch/stefan/7916127/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045395 none CNC(=O)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', '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', '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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 201, 135, 127, 41, 41, 41, 27, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 154, 154, 153, 153, 127, 127, 41, 27, 27, 18, 18, 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: 908 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045395 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045395 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045395/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045395 Building REAL250005045396 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045396' /scratch/stefan/7916127/working/building/REAL250005045396 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045396 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045396/0 /scratch/stefan/7916127/working/building/REAL250005045396 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/525 `/scratch/stefan/7916127/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045396 none COC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 155, 155, 155, 155, 113, 113, 113, 45, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 155, 161, 161, 161, 113, 45, 45, 28, 28, 9, 1, 155] 161 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]) 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: REAL250005045396 none COC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 63, 147, 147, 147, 155, 155, 155, 155, 155, 1, 3, 3, 3, 9, 40, 40, 63, 63, 147, 155, 1] 161 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045396 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045396 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045396/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045396 Building REAL250005045397 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045397' /scratch/stefan/7916127/working/building/REAL250005045397 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045397 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045397/0 /scratch/stefan/7916127/working/building/REAL250005045397 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/526 `/scratch/stefan/7916127/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045397 none COC(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 115, 192, 125, 49, 49, 49, 19, 16, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 192, 192, 192, 184, 192, 192, 192, 146, 146, 125, 125, 49, 19, 19, 16, 16, 5, 1] 192 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: 976 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045397 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045397 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045397/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045397 Building REAL250005045398 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045398' /scratch/stefan/7916127/working/building/REAL250005045398 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045398 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045398/0 /scratch/stefan/7916127/working/building/REAL250005045398 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/527 `/scratch/stefan/7916127/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005045398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045398 none CCC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 157, 157, 157, 143, 143, 143, 54, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 143, 54, 54, 30, 30, 7, 1, 157] 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]) total number of confs: 751 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045398 none CCC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 5, 5, 5, 27, 46, 143, 143, 143, 157, 157, 157, 157, 157, 1, 1, 8, 8, 8, 8, 8, 5, 27, 27, 46, 46, 143, 157, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 33, 19, 20] set([0, 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]) total number of confs: 492 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045398 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045398 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045398/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045398 Building REAL250005045399 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045399' /scratch/stefan/7916127/working/building/REAL250005045399 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045399 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045399/0 /scratch/stefan/7916127/working/building/REAL250005045399 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/528 `/scratch/stefan/7916127/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=C(F)C=N1)C1=CC(=O)[N-]O1) `REAL250005045399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045399 none O=C(NCCNC(=O)C1=CC=C(F)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 19, 37, 37, 37, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 4, 14, 14, 19, 19, 37, 63, 63, 63, 1] 63 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045399 none O=C(NCCNC(=O)C1=CC=C(F)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 43, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 43, 43, 34, 34, 10, 1, 1, 1, 63] 63 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045399 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045399 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045399/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045399 Building REAL250005045400 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045400' /scratch/stefan/7916127/working/building/REAL250005045400 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045400 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045400/0 /scratch/stefan/7916127/working/building/REAL250005045400 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/529 `/scratch/stefan/7916127/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N) `REAL250005045400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045400 none CN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 174, 113, 113, 113, 48, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 174, 113, 48, 48, 32, 32, 11, 1, 174, 174] 174 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: 472 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: REAL250005045400 none CN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 12, 12, 12, 61, 89, 162, 163, 162, 174, 174, 174, 174, 174, 1, 1, 2, 2, 2, 1, 12, 61, 61, 89, 89, 163, 174, 2, 2] 174 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 635 number of broken/clashed sets: 64 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045400 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045400 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045400/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045400 Building REAL250005045401 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045401' /scratch/stefan/7916127/working/building/REAL250005045401 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045401 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045401/0 /scratch/stefan/7916127/working/building/REAL250005045401 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/530 `/scratch/stefan/7916127/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CN=C1)C1=CC(=O)[N-]O1) `REAL250005045401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045401 none O=C(NCCNC(=O)C1=CN=CN=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 32, 44, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 11, 32, 32, 44, 44, 79, 79, 79, 79, 1] 79 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045401 none O=C(NCCNC(=O)C1=CN=CN=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [74, 74, 32, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 74, 79, 79, 79, 79, 79, 74, 32, 32, 16, 16, 4, 1, 1, 1, 79] 79 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045401 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045401 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045401/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045401 Building REAL250005045402 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045402' /scratch/stefan/7916127/working/building/REAL250005045402 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045402 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045402/0 /scratch/stefan/7916127/working/building/REAL250005045402 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/531 `/scratch/stefan/7916127/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC=CC=C1O)C1=CC(=O)[N-]O1) `REAL250005045402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045402 none O=C(NCCNC(=O)C1=NC=CC=C1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 16, 21, 51, 51, 51, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 5, 16, 16, 21, 21, 51, 70, 70, 70, 140, 1] 140 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 340 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: REAL250005045402 none O=C(NCCNC(=O)C1=NC=CC=C1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 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 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 42, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 69, 70, 70, 70, 70, 70, 69, 42, 42, 32, 32, 9, 1, 1, 1, 2, 70] 140 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31]) total number of confs: 270 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045402 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045402/1 /scratch/stefan/7916127/working/building/REAL250005045402 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/532 `/scratch/stefan/7916127/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC=CC=C1[O-])C1=CC(=O)[N-]O1) `REAL250005045402.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045402/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045402 none O=C(NCCNC(=O)C1=NC=CC=C1[O-])C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [4, 1, 4, 4, 22, 31, 53, 53, 53, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 4, 22, 22, 31, 31, 53, 65, 65, 65, 1] 65 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005045402 none O=C(NCCNC(=O)C1=NC=CC=C1[O-])C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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, 63, 43, 37, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 63, 65, 65, 65, 65, 65, 65, 43, 43, 37, 37, 9, 1, 1, 1, 65] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045402 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045402 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045402/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045402/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045402 Building REAL250005045403 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045403' /scratch/stefan/7916127/working/building/REAL250005045403 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045403 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045403/0 /scratch/stefan/7916127/working/building/REAL250005045403 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/533 `/scratch/stefan/7916127/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CCOCC1)C1=CC(=O)[N-]O1) `REAL250005045403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045403 none O=C(NCCNC(=O)C1=CCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 1, 9, 9, 33, 49, 92, 92, 92, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 1, 9, 33, 33, 49, 49, 92, 128, 128, 128, 128, 128, 128, 128, 1] 128 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045403 none O=C(NCCNC(=O)C1=CCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [123, 123, 82, 58, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 123, 128, 128, 128, 128, 128, 123, 82, 82, 58, 58, 11, 1, 1, 1, 1, 1, 1, 1, 128] 128 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045403 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045403 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045403/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045403 Building REAL250005045404 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045404' /scratch/stefan/7916127/working/building/REAL250005045404 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045404 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045404/0 /scratch/stefan/7916127/working/building/REAL250005045404 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/534 `/scratch/stefan/7916127/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=COC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045404 none O=C(CC1=COC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 104, 201, 201, 201, 201, 27, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 104, 104, 201, 201, 201, 57, 27, 27, 18, 18, 4, 1] 201 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]) total number of confs: 586 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045404 none O=C(CC1=COC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 15, 15, 81, 105, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 1, 1, 1, 15, 81, 81, 105, 105, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 729 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045404 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045404 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045404/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045404 Building REAL250005045405 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045405' /scratch/stefan/7916127/working/building/REAL250005045405 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045405 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045405/0 /scratch/stefan/7916127/working/building/REAL250005045405 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/535 `/scratch/stefan/7916127/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005045405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045405 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 69, 69, 69, 41, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 69, 41, 41, 28, 28, 9, 1, 71] 71 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]) 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: REAL250005045405 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 21, 34, 65, 65, 65, 71, 71, 71, 71, 71, 1, 1, 2, 2, 2, 4, 20, 20, 34, 34, 65, 71, 1] 71 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045405 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045405 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045405/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045405 Building REAL250005045406 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045406' /scratch/stefan/7916127/working/building/REAL250005045406 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045406 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045406/0 /scratch/stefan/7916127/working/building/REAL250005045406 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/536 `/scratch/stefan/7916127/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CCCCCC1)C1=CC(=O)[N-]O1) `REAL250005045406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045406 none O=C(NCCNC(=O)C1=CCCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 29, 46, 115, 115, 115, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 29, 29, 46, 46, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 502 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: REAL250005045406 none O=C(NCCNC(=O)C1=CCCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [197, 196, 120, 76, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 196, 201, 201, 201, 201, 201, 197, 120, 120, 76, 76, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 755 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045406 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045406 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045406/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045406 Building REAL250005045407 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045407' /scratch/stefan/7916127/working/building/REAL250005045407 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045407 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045407/0 /scratch/stefan/7916127/working/building/REAL250005045407 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/537 `/scratch/stefan/7916127/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045407 none C[C@H](NC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 95, 195, 195, 201, 201, 201, 95, 95, 38, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 195, 195, 193, 201, 201, 201, 95, 38, 38, 27, 27, 9, 1] 201 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]) total number of confs: 784 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045407 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045407 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045407/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045407 Building REAL250005045408 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045408' /scratch/stefan/7916127/working/building/REAL250005045408 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045408 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045408/0 /scratch/stefan/7916127/working/building/REAL250005045408 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/538 `/scratch/stefan/7916127/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1OCCCO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045408 none O=C(CC1OCCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 178, 201, 201, 201, 201, 201, 31, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 179, 179, 201, 201, 201, 201, 201, 201, 201, 99, 31, 31, 20, 20, 4, 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: 737 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045408 none O=C(CC1OCCCO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens 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, 8, 1, 1, 1, 1, 1, 1, 1, 25, 25, 85, 129, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 25, 85, 85, 129, 129, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 793 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045408 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045408 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045408/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045408 Building REAL250005045409 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045409' /scratch/stefan/7916127/working/building/REAL250005045409 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045409 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045409/0 /scratch/stefan/7916127/working/building/REAL250005045409 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/539 `/scratch/stefan/7916127/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005045409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045409 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 95, 95, 95, 50, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 95, 50, 50, 32, 32, 11, 1, 137] 137 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]) 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: REAL250005045409 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 28, 63, 126, 126, 126, 137, 137, 137, 137, 137, 1, 1, 2, 2, 2, 1, 5, 28, 28, 63, 63, 126, 137, 1] 137 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 501 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045409 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045409 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045409/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045409 Building REAL250005045410 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045410' /scratch/stefan/7916127/working/building/REAL250005045410 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045410 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045410/0 /scratch/stefan/7916127/working/building/REAL250005045410 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/540 `/scratch/stefan/7916127/working/3D/540' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1=CC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045410 none O=C(C=CC1=CC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 164, 164, 201, 201, 201, 201, 43, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 87, 43, 43, 26, 26, 9, 1] 201 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]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045410 none O=C(C=CC1=CC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 12, 12, 1, 1, 1, 1, 1, 1, 52, 52, 123, 158, 199, 199, 199, 201, 201, 201, 201, 201, 12, 12, 1, 1, 1, 1, 52, 123, 123, 158, 158, 199, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045410 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045410 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045410/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045410 Building REAL250005045411 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045411' /scratch/stefan/7916127/working/building/REAL250005045411 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045411 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045411/0 /scratch/stefan/7916127/working/building/REAL250005045411 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/541 `/scratch/stefan/7916127/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)C=C1) `REAL250005045411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045411 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)C=C1 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', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 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, 43, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 115, 43, 43, 28, 28, 6, 1, 201, 201, 201, 201, 201] 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, 35]) total number of confs: 510 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: REAL250005045411 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)C=C1 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', 'N.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 49, 85, 199, 199, 199, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 11, 49, 49, 85, 85, 199, 201, 2, 2, 2, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 35, 34, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 713 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045411 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045411 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045411/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045411 Building REAL250005045412 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045412' /scratch/stefan/7916127/working/building/REAL250005045412 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045412 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045412/0 /scratch/stefan/7916127/working/building/REAL250005045412 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/542 `/scratch/stefan/7916127/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN=N1) `REAL250005045412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045412 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 57, 57, 57, 37, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 57, 37, 37, 26, 26, 9, 1, 113] 113 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]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045412 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 33, 55, 107, 107, 107, 113, 113, 113, 113, 113, 1, 1, 1, 2, 2, 2, 1, 5, 33, 33, 55, 55, 107, 113, 1] 113 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045412 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045412 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045412/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045412 Building REAL250005045413 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045413' /scratch/stefan/7916127/working/building/REAL250005045413 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045413 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045413/0 /scratch/stefan/7916127/working/building/REAL250005045413 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/543 `/scratch/stefan/7916127/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=CN=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045413 none O=C(CCN1C=CN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 129, 151, 201, 201, 201, 201, 26, 19, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 129, 129, 151, 151, 201, 201, 71, 26, 26, 19, 19, 6, 1] 201 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]) total number of confs: 685 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045413 none O=C(CCN1C=CN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 17, 9, 1, 1, 1, 1, 1, 1, 67, 67, 131, 156, 201, 201, 201, 201, 201, 201, 201, 201, 17, 17, 9, 9, 1, 1, 67, 135, 135, 155, 155, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 792 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045413 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045413 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045413/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045413 Building REAL250005045414 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045414' /scratch/stefan/7916127/working/building/REAL250005045414 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045414 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045414/0 /scratch/stefan/7916127/working/building/REAL250005045414 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/544 `/scratch/stefan/7916127/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045414 none CC(=O)N1CC(C(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 201, 167, 167, 92, 92, 92, 32, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 167, 201, 201, 201, 167, 167, 167, 92, 32, 32, 20, 20, 6, 1, 167, 167] 201 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: 648 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: REAL250005045414 none CC(=O)N1CC(C(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 13, 13, 13, 60, 90, 163, 163, 163, 167, 167, 167, 167, 167, 1, 3, 3, 3, 1, 1, 1, 13, 60, 60, 90, 90, 163, 167, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 5, 6, 35, 20, 24, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 618 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045414 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045414 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045414/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045414 Building REAL250005045415 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045415' /scratch/stefan/7916127/working/building/REAL250005045415 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045415 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045415/0 /scratch/stefan/7916127/working/building/REAL250005045415 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/545 `/scratch/stefan/7916127/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1OC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC1=O) `REAL250005045415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045415 none CN1OC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 93, 93, 93, 41, 25, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 93, 41, 41, 25, 25, 10, 1, 115] 115 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]) total number of confs: 352 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045415 none CN1OC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'O.3', '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.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 12, 12, 12, 39, 57, 107, 107, 107, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 12, 38, 38, 57, 57, 107, 115, 1] 115 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 21, 22, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 390 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045415 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045415 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045415/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045415 Building REAL250005045416 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045416' /scratch/stefan/7916127/working/building/REAL250005045416 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045416 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045416/0 /scratch/stefan/7916127/working/building/REAL250005045416 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/546 `/scratch/stefan/7916127/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045416 none CCC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 186, 145, 185, 39, 39, 39, 29, 19, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 186, 186, 186, 186, 145, 145, 39, 29, 29, 19, 19, 4, 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: 886 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045416 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045416 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045416/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045416 Building REAL250005045417 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045417' /scratch/stefan/7916127/working/building/REAL250005045417 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045417 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045417/0 /scratch/stefan/7916127/working/building/REAL250005045417 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/547 `/scratch/stefan/7916127/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045417 none COC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 131, 72, 72, 72, 32, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 201, 201, 201, 131, 131, 72, 32, 32, 21, 21, 4, 1, 200, 200, 200, 200, 200, 200] 201 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: 777 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: REAL250005045417 none COC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 9, 32, 32, 32, 108, 126, 199, 200, 199, 200, 200, 200, 200, 200, 1, 1, 1, 6, 6, 6, 9, 9, 32, 108, 108, 126, 126, 200, 200, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 34, 18, 19, 20, 38] set([0, 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, 32]) total number of confs: 752 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045417 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045417 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045417/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045417 Building REAL250005045418 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045418' /scratch/stefan/7916127/working/building/REAL250005045418 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045418 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045418/0 /scratch/stefan/7916127/working/building/REAL250005045418 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/548 `/scratch/stefan/7916127/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045418 none CC1OCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 119, 119, 119, 57, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 119, 57, 57, 37, 37, 11, 1] 164 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: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045418 none CC1OCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 43, 74, 153, 153, 153, 164, 164, 164, 164, 164, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 43, 43, 74, 74, 153, 164] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045418 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045418 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045418/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045418 Building REAL250005045419 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045419' /scratch/stefan/7916127/working/building/REAL250005045419 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045419 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045419/0 /scratch/stefan/7916127/working/building/REAL250005045419 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/549 `/scratch/stefan/7916127/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045419 none C#CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 123, 37, 37, 37, 17, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 191, 191, 153, 153, 123, 123, 37, 17, 17, 11, 11, 3, 1] 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]) total number of confs: 984 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045419 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045419 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045419/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045419 Building REAL250005045420 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045420' /scratch/stefan/7916127/working/building/REAL250005045420 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045420 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045420/0 /scratch/stefan/7916127/working/building/REAL250005045420 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/550 `/scratch/stefan/7916127/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=C(Cl)OC=C1)C1=CC(=O)[N-]O1) `REAL250005045420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045420 none O=C(NCCNC(=O)C1=C(Cl)OC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 34, 57, 125, 125, 125, 199, 199, 199, 199, 199, 1, 1, 1, 1, 1, 1, 11, 34, 34, 57, 57, 125, 199, 199, 1] 199 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045420 none O=C(NCCNC(=O)C1=C(Cl)OC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 79, 39, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 187, 199, 199, 199, 199, 199, 187, 79, 79, 39, 39, 7, 1, 1, 199] 199 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 669 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045420 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045420 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045420/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045420 Building REAL250005045421 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045421' /scratch/stefan/7916127/working/building/REAL250005045421 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045421 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045421/0 /scratch/stefan/7916127/working/building/REAL250005045421 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/551 `/scratch/stefan/7916127/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045421 none C=CC(C)(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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 318 conformations in input total number of sets (complete confs): 318 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 84, 105, 106, 60, 60, 60, 25, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 106, 106, 106, 106, 106, 106, 318, 84, 84, 60, 25, 25, 17, 17, 4, 1] 318 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: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045421 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045421 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045421/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045421 Building REAL250005045422 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045422' /scratch/stefan/7916127/working/building/REAL250005045422 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045422 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045422/0 /scratch/stefan/7916127/working/building/REAL250005045422 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/552 `/scratch/stefan/7916127/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NS1) `REAL250005045422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045422 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 81, 81, 81, 41, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 85, 85, 85, 85, 85, 85, 81, 41, 41, 26, 26, 9, 1] 85 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]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045422 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 28, 41, 81, 81, 81, 85, 85, 85, 85, 85, 1, 1, 2, 2, 2, 1, 8, 28, 28, 41, 41, 81, 85] 85 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 294 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045422 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045422 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045422/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045422 Building REAL250005045423 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045423' /scratch/stefan/7916127/working/building/REAL250005045423 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045423 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045423/0 /scratch/stefan/7916127/working/building/REAL250005045423 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/553 `/scratch/stefan/7916127/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045423 none CCN1C=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 131, 131, 131, 131, 131, 122, 122, 122, 39, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 131, 131, 122, 39, 39, 25, 25, 4, 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: 818 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045423 none CCN1C=CN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 27, 49, 128, 128, 128, 131, 131, 131, 131, 131, 6, 6, 6, 6, 6, 1, 1, 5, 27, 27, 49, 49, 128, 131] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27] set([0, 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: 443 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045423 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045423 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045423/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045423 Building REAL250005045424 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045424' /scratch/stefan/7916127/working/building/REAL250005045424 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045424 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045424/0 /scratch/stefan/7916127/working/building/REAL250005045424 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/554 `/scratch/stefan/7916127/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCOCC1)C1=CC(=O)[N-]O1) `REAL250005045424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045424 none O=C(NCCNC(=O)C1CCCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 50, 122, 122, 122, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 32, 32, 50, 50, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 653 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: REAL250005045424 none O=C(NCCNC(=O)C1CCCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 193, 106, 66, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 194, 106, 106, 66, 66, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 720 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045424 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045424 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045424/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045424 Building REAL250005045425 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045425' /scratch/stefan/7916127/working/building/REAL250005045425 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045425 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045425/0 /scratch/stefan/7916127/working/building/REAL250005045425 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/555 `/scratch/stefan/7916127/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045425 none O=C(CCC1=NC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 170, 192, 201, 201, 201, 201, 31, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 171, 171, 192, 192, 201, 201, 201, 84, 31, 31, 20, 20, 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: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045425 none O=C(CCC1=NC=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'N.am', '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: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 10, 6, 1, 1, 1, 1, 1, 1, 50, 50, 108, 135, 197, 197, 197, 201, 201, 201, 201, 201, 10, 10, 6, 6, 1, 1, 1, 50, 108, 108, 135, 135, 197, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045425 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045425 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045425/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045425 Building REAL250005045426 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045426' /scratch/stefan/7916127/working/building/REAL250005045426 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045426 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045426/0 /scratch/stefan/7916127/working/building/REAL250005045426 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/556 `/scratch/stefan/7916127/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC(O)CC1)C1=CC(=O)[N-]O1) `REAL250005045426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045426 none O=C(NCCNC(=O)C1CCC(O)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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] 1 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: [9, 1, 9, 9, 32, 45, 116, 116, 116, 183, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 1, 9, 32, 32, 45, 45, 116, 183, 183, 183, 183, 183, 183, 549, 183, 183, 183, 183, 1] 549 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: 1136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045426 none O=C(NCCNC(=O)C1CCC(O)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 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] 1 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: [174, 173, 102, 67, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 173, 183, 183, 183, 183, 183, 174, 102, 102, 67, 67, 12, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 183] 549 rigid atoms, others: [32, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 668 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045426 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045426 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045426/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045426 Building REAL250005045427 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045427' /scratch/stefan/7916127/working/building/REAL250005045427 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045427 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045427/0 /scratch/stefan/7916127/working/building/REAL250005045427 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/557 `/scratch/stefan/7916127/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045427 none CC(C)(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [199, 173, 201, 201, 98, 98, 98, 44, 29, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 173, 173, 98, 44, 44, 29, 29, 7, 1] 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]) total number of confs: 1436 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045427 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045427 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045427/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045427 Building REAL250005045428 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045428' /scratch/stefan/7916127/working/building/REAL250005045428 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045428 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045428/0 /scratch/stefan/7916127/working/building/REAL250005045428 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/558 `/scratch/stefan/7916127/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045428 none CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [154, 154, 150, 154, 154, 95, 95, 95, 43, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 150, 154, 95, 43, 43, 30, 30, 7, 1] 154 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]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045428 none CC1=CC=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 81, 144, 146, 144, 154, 154, 154, 154, 154, 1, 2, 2, 2, 1, 1, 10, 52, 52, 81, 81, 146, 154] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045428 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045428 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045428/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045428 Building REAL250005045429 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045429' /scratch/stefan/7916127/working/building/REAL250005045429 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045429 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045429/0 /scratch/stefan/7916127/working/building/REAL250005045429 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/559 `/scratch/stefan/7916127/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045429 none COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', '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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 1, 8, 32, 32, 32, 104, 130, 200, 201, 200, 201, 201, 201, 201, 201, 1, 1, 1, 17, 17, 17, 8, 32, 104, 104, 130, 130, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 34, 17, 18, 19, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 763 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045429 none COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', '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, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 154, 81, 81, 81, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 154, 201, 201, 158, 158, 158, 154, 81, 30, 30, 19, 19, 4, 1, 201, 201, 201, 201, 201] 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, 35]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045429 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045429 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045429/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045429 Building REAL250005045430 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045430' /scratch/stefan/7916127/working/building/REAL250005045430 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045430 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045430/0 /scratch/stefan/7916127/working/building/REAL250005045430 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/560 `/scratch/stefan/7916127/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CO1) `REAL250005045430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045430 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 188, 188, 98, 98, 98, 39, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 188, 188, 188, 201, 201, 201, 201, 201, 98, 39, 39, 26, 26, 7, 1, 188, 188] 201 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: 524 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: REAL250005045430 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CO1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 9, 9, 9, 54, 81, 178, 180, 178, 188, 188, 188, 188, 188, 1, 1, 1, 6, 6, 6, 6, 6, 9, 54, 54, 81, 81, 180, 188, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 34, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 652 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045430 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045430 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045430/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045430 Building REAL250005045431 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045431' /scratch/stefan/7916127/working/building/REAL250005045431 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045431 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045431/0 /scratch/stefan/7916127/working/building/REAL250005045431 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/561 `/scratch/stefan/7916127/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=C1) `REAL250005045431.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045431 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=C1 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', 'N.pl3', 'C.2', 'C.2', '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, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 101, 101, 101, 49, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 184, 184, 184, 184, 184, 184, 101, 49, 49, 32, 32, 11, 1, 184, 184, 184] 184 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: 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: REAL250005045431 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=C1 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', 'N.pl3', 'C.2', 'C.2', '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, 8, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 184 conformations in input total number of sets (complete confs): 184 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 12, 12, 12, 54, 93, 176, 176, 176, 184, 184, 184, 184, 184, 1, 1, 1, 2, 2, 2, 12, 54, 54, 93, 93, 176, 184, 1, 1, 1] 184 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 680 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045431 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045431 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045431/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045431 Building REAL250005045432 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045432' /scratch/stefan/7916127/working/building/REAL250005045432 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045432 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045432/0 /scratch/stefan/7916127/working/building/REAL250005045432 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/562 `/scratch/stefan/7916127/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045432.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045432 none CN1N=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 89, 89, 89, 39, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 89, 39, 39, 26, 26, 9, 1] 107 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]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045432 none CN1N=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 61, 103, 103, 103, 107, 107, 107, 107, 107, 2, 2, 2, 1, 10, 40, 40, 61, 61, 103, 107] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 398 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045432 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045432 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045432/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045432 Building REAL250005045433 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045433' /scratch/stefan/7916127/working/building/REAL250005045433 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045433 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045433/0 /scratch/stefan/7916127/working/building/REAL250005045433 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/563 `/scratch/stefan/7916127/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1COC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045433.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045433 none O=C(NCCNC(=O)C1COC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 12, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 31, 42, 98, 98, 98, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 1, 10, 31, 31, 42, 42, 98, 150, 150, 150, 150, 1] 150 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 509 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: REAL250005045433 none O=C(NCCNC(=O)C1COC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 5, 12, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 78, 59, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 142, 150, 150, 150, 150, 150, 142, 78, 78, 59, 59, 12, 1, 1, 1, 1, 150] 150 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30]) total number of confs: 537 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045433 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045433 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045433/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045433 Building REAL250005045434 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045434' /scratch/stefan/7916127/working/building/REAL250005045434 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045434 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045434/0 /scratch/stefan/7916127/working/building/REAL250005045434 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/564 `/scratch/stefan/7916127/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045434.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045434 none CCCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 181, 173, 127, 44, 127, 44, 44, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 176, 176, 127, 127, 127, 127, 44, 25, 25, 16, 16, 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: 978 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045434 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045434 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045434/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045434 Building REAL250005045435 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045435' /scratch/stefan/7916127/working/building/REAL250005045435 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045435 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045435/0 /scratch/stefan/7916127/working/building/REAL250005045435 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/565 `/scratch/stefan/7916127/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045435.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045435 none CC1CC(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 87, 87, 87, 35, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 87, 35, 35, 24, 24, 8, 1] 110 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]) total number of confs: 364 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: REAL250005045435 none CC1CC(C)C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 27, 44, 107, 107, 107, 110, 110, 110, 110, 110, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 4, 27, 27, 44, 44, 107, 110] 110 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25, 26, 27, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 383 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045435 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045435 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045435/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045435 Building REAL250005045436 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045436' /scratch/stefan/7916127/working/building/REAL250005045436 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045436 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045436/0 /scratch/stefan/7916127/working/building/REAL250005045436 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/566 `/scratch/stefan/7916127/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1C[C@@H]1C(F)F)C1=CC(=O)[N-]O1) `REAL250005045436.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045436 none O=C(NCCNC(=O)[C@H]1C[C@@H]1C(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 12, 22, 64, 64, 64, 185, 185, 185, 185, 185, 201, 201, 1, 1, 1, 1, 1, 1, 3, 12, 12, 22, 22, 64, 185, 185, 201, 1] 201 rigid atoms, others: [1, 16, 17, 18, 19, 20, 21, 31] 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]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045436 none O=C(NCCNC(=O)[C@H]1C[C@@H]1C(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 178, 78, 63, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 9, 9, 182, 185, 185, 185, 185, 185, 182, 78, 78, 63, 63, 13, 1, 1, 9, 185] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 648 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045436 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045436 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045436/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045436 Building REAL250005045437 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045437' /scratch/stefan/7916127/working/building/REAL250005045437 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045437 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045437/0 /scratch/stefan/7916127/working/building/REAL250005045437 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/567 `/scratch/stefan/7916127/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045437.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045437 none CC1=COC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 118, 118, 118, 46, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 118, 46, 46, 28, 28, 6, 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: 514 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: REAL250005045437 none CC1=COC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 11, 62, 98, 199, 199, 199, 201, 201, 201, 201, 201, 2, 2, 2, 1, 2, 2, 2, 12, 62, 62, 98, 98, 199, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 743 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045437 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045437 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045437/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045437 Building REAL250005045438 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045438' /scratch/stefan/7916127/working/building/REAL250005045438 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045438 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045438/0 /scratch/stefan/7916127/working/building/REAL250005045438 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/568 `/scratch/stefan/7916127/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045438.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045438 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [126, 126, 126, 126, 97, 97, 97, 49, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 126, 126, 126, 126, 126, 126, 126, 126, 126, 126, 97, 49, 49, 32, 32, 9, 1, 126, 126] 126 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: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045438 none CC1(C)CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 40, 112, 112, 112, 126, 126, 126, 126, 126, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 22, 22, 40, 40, 112, 126, 1, 1] 126 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 36, 26, 27, 28, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045438 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045438 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045438/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045438 Building REAL250005045439 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045439' /scratch/stefan/7916127/working/building/REAL250005045439 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045439 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045439/0 /scratch/stefan/7916127/working/building/REAL250005045439 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/569 `/scratch/stefan/7916127/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1) `REAL250005045439.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045439 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need 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, 85, 85, 85, 32, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 152, 152, 152, 201, 201, 201, 201, 201, 85, 32, 32, 20, 20, 4, 1, 152, 152, 152] 201 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: 681 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: REAL250005045439 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'C.2', 'N.pl3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 12, 12, 12, 53, 74, 146, 148, 146, 152, 152, 152, 152, 152, 1, 1, 1, 6, 6, 6, 6, 6, 12, 53, 53, 74, 74, 148, 152, 1, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 35, 33, 34, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 554 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045439 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045439 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045439/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045439 Building REAL250005045440 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045440' /scratch/stefan/7916127/working/building/REAL250005045440 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045440 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045440/0 /scratch/stefan/7916127/working/building/REAL250005045440 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/570 `/scratch/stefan/7916127/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045440.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045440 none CC(C)[C@@H](O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 201, 103, 185, 185, 103, 103, 36, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 555, 103, 36, 36, 22, 22, 4, 1] 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]) total number of confs: 1369 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045440 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045440 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045440/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045440 Building REAL250005045441 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045441' /scratch/stefan/7916127/working/building/REAL250005045441 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045441 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045441/0 /scratch/stefan/7916127/working/building/REAL250005045441 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/571 `/scratch/stefan/7916127/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045441.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045441 none CCOC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 166, 166, 166, 73, 73, 73, 32, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 166, 201, 201, 201, 201, 201, 166, 166, 166, 166, 73, 32, 32, 22, 22, 4, 1, 166, 166] 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, 37, 38]) total number of confs: 573 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: REAL250005045441 none CCOC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 13, 13, 13, 39, 48, 142, 142, 142, 166, 166, 166, 166, 166, 1, 10, 10, 10, 10, 10, 1, 1, 1, 1, 13, 39, 39, 48, 48, 142, 166, 1, 1] 201 rigid atoms, others: [2, 3, 4, 5, 6, 38, 20, 26, 27, 28, 29, 37] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 517 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045441 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045441 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045441/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045441 Building REAL250005045442 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045442' /scratch/stefan/7916127/working/building/REAL250005045442 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045442 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045442/0 /scratch/stefan/7916127/working/building/REAL250005045442 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/572 `/scratch/stefan/7916127/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005045442.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045442 none CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 51, 51, 51, 29, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 126, 126, 51, 29, 29, 18, 18, 4, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 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: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045442 none CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 10, 25, 25, 25, 101, 120, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 10, 10, 25, 101, 101, 120, 120, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 33, 40, 39, 34, 17, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045442 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045442 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045442/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045442 Building REAL250005045443 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045443' /scratch/stefan/7916127/working/building/REAL250005045443 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045443 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045443/0 /scratch/stefan/7916127/working/building/REAL250005045443 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/573 `/scratch/stefan/7916127/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1) `REAL250005045443.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045443 none CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 72, 72, 72, 35, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 72, 35, 35, 22, 22, 5, 1] 78 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]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045443 none CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', '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', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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, 7, 7, 7, 27, 43, 74, 74, 74, 78, 78, 78, 78, 78, 1, 1, 2, 2, 2, 1, 7, 27, 27, 43, 43, 74, 78] 78 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 291 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045443 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045443 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045443/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045443 Building REAL250005045444 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045444' /scratch/stefan/7916127/working/building/REAL250005045444 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045444 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045444/0 /scratch/stefan/7916127/working/building/REAL250005045444 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/574 `/scratch/stefan/7916127/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045444.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045444 none CC1=NN=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 148, 79, 79, 79, 32, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 148, 148, 79, 32, 32, 20, 20, 4, 1] 201 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]) total number of confs: 651 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045444 none CC1=NN=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 39, 39, 39, 103, 129, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 8, 8, 39, 103, 103, 129, 129, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045444 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045444 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045444/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045444 Building REAL250005045445 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045445' /scratch/stefan/7916127/working/building/REAL250005045445 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045445 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045445/0 /scratch/stefan/7916127/working/building/REAL250005045445 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/575 `/scratch/stefan/7916127/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045445.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045445 none CN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 78, 78, 78, 38, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 116, 116, 116, 116, 116, 78, 38, 38, 24, 24, 8, 1] 116 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]) total number of confs: 343 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045445 none CN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 38, 63, 107, 109, 107, 116, 116, 116, 116, 116, 1, 2, 2, 2, 1, 7, 37, 37, 63, 63, 109, 116] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 436 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045445 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045445 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045445/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045445 Building REAL250005045446 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045446' /scratch/stefan/7916127/working/building/REAL250005045446 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045446 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045446/0 /scratch/stefan/7916127/working/building/REAL250005045446 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/576 `/scratch/stefan/7916127/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045446.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045446 none CNC(=O)NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need 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, 189, 191, 175, 138, 71, 71, 71, 25, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 189, 175, 175, 138, 138, 71, 25, 25, 18, 18, 4, 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: 824 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045446 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045446 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045446/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045446 Building REAL250005045447 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045447' /scratch/stefan/7916127/working/building/REAL250005045447 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045447 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045447/0 /scratch/stefan/7916127/working/building/REAL250005045447 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/577 `/scratch/stefan/7916127/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=C(F)C=CS1)C1=CC(=O)[N-]O1) `REAL250005045447.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045447 none O=C(NCCNC(=O)C1=C(F)C=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 34, 52, 112, 112, 112, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 34, 34, 52, 52, 112, 201, 201, 1] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 530 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045447 none O=C(NCCNC(=O)C1=C(F)C=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 114, 79, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 114, 114, 78, 78, 13, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045447 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045447 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045447/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045447 Building REAL250005045448 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045448' /scratch/stefan/7916127/working/building/REAL250005045448 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045448 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045448/0 /scratch/stefan/7916127/working/building/REAL250005045448 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/578 `/scratch/stefan/7916127/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045448.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045448 none CCN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 146, 146, 146, 146, 136, 135, 136, 54, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 146, 195, 195, 195, 195, 195, 146, 136, 54, 54, 35, 35, 7, 1] 195 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]) total number of confs: 755 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045448 none CCN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 42, 129, 129, 129, 146, 146, 146, 146, 146, 1, 9, 9, 9, 9, 9, 1, 4, 23, 23, 42, 42, 129, 146] 195 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 471 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045448 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045448 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045448/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045448 Building REAL250005045449 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045449' /scratch/stefan/7916127/working/building/REAL250005045449 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045449 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045449/0 /scratch/stefan/7916127/working/building/REAL250005045449 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/579 `/scratch/stefan/7916127/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045449.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045449 none CC(C)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 35, 67, 67, 67, 103, 103, 198, 201, 198, 201, 201, 201, 201, 201, 1, 1, 1, 10, 10, 10, 10, 10, 10, 35, 35, 67, 103, 103, 103, 103, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 36, 37, 38, 39, 40, 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, 32, 33, 34, 35]) total number of confs: 732 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: REAL250005045449 none CC(C)(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 63, 122, 28, 28, 28, 22, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 123, 201, 201, 123, 123, 123, 123, 123, 123, 63, 63, 28, 22, 22, 15, 15, 4, 1, 201, 201, 201, 201, 201] 201 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, 39, 40]) total number of confs: 826 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045449 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045449 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045449/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045449 Building REAL250005045450 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045450' /scratch/stefan/7916127/working/building/REAL250005045450 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045450 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045450/0 /scratch/stefan/7916127/working/building/REAL250005045450 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/580 `/scratch/stefan/7916127/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1N=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045450.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045450 none CCN1N=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 147, 147, 147, 147, 109, 109, 109, 37, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 147, 109, 37, 37, 22, 22, 4, 1] 201 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]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045450 none CCN1N=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 46, 73, 143, 145, 144, 147, 147, 147, 147, 147, 6, 6, 6, 6, 6, 1, 10, 46, 46, 73, 73, 145, 147] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045450 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045450 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045450/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045450 Building REAL250005045451 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045451' /scratch/stefan/7916127/working/building/REAL250005045451 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045451 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045451/0 /scratch/stefan/7916127/working/building/REAL250005045451 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/581 `/scratch/stefan/7916127/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CSC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045451.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045451 none CC1=CSC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 97, 97, 97, 41, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 127, 127, 127, 127, 127, 97, 41, 41, 28, 28, 11, 1, 127] 127 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]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045451 none CC1=CSC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'S.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 43, 71, 119, 119, 119, 127, 127, 127, 127, 127, 1, 2, 2, 2, 1, 11, 43, 43, 71, 71, 119, 127, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 475 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045451 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045451 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045451/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045451 Building REAL250005045452 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045452' /scratch/stefan/7916127/working/building/REAL250005045452 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045452 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045452/0 /scratch/stefan/7916127/working/building/REAL250005045452 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/582 `/scratch/stefan/7916127/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC1(F)F)C1=CC(=O)[N-]O1) `REAL250005045452.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045452 none O=C(NCCNC(=O)C1CC1(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 51, 115, 115, 115, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 32, 32, 51, 51, 115, 201, 201, 201, 1] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045452 none O=C(NCCNC(=O)C1CC1(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 194, 112, 73, 13, 13, 1, 13, 1, 1, 1, 1, 1, 194, 201, 201, 201, 201, 201, 195, 112, 112, 73, 73, 13, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045452 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045452 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045452/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045452 Building REAL250005045453 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045453' /scratch/stefan/7916127/working/building/REAL250005045453 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045453 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045453/0 /scratch/stefan/7916127/working/building/REAL250005045453 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/583 `/scratch/stefan/7916127/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045453.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045453 none CCC(C)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 125, 125, 125, 91, 91, 91, 43, 29, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 125, 125, 125, 125, 91, 43, 43, 29, 29, 7, 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: 902 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045453 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045453 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045453/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045453 Building REAL250005045454 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045454' /scratch/stefan/7916127/working/building/REAL250005045454 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045454 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045454/0 /scratch/stefan/7916127/working/building/REAL250005045454 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/584 `/scratch/stefan/7916127/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045454.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045454 none CC1=CN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 175, 201, 201, 118, 118, 118, 48, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 118, 48, 48, 34, 34, 11, 1] 201 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]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045454 none CC1=CN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 63, 105, 193, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 10, 63, 63, 105, 105, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045454 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045454 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045454/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045454 Building REAL250005045455 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045455' /scratch/stefan/7916127/working/building/REAL250005045455 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045455 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045455/0 /scratch/stefan/7916127/working/building/REAL250005045455 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/585 `/scratch/stefan/7916127/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C#CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045455.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045455 none CC(C)C#CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 58, 35, 24, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 35, 35, 24, 24, 7, 1] 58 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]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045455 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045455 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045455/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045455 Building REAL250005045456 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045456' /scratch/stefan/7916127/working/building/REAL250005045456 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045456 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045456/0 /scratch/stefan/7916127/working/building/REAL250005045456 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/586 `/scratch/stefan/7916127/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CS1) `REAL250005045456.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045456 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CS1 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.2', 'C.2', 'S.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 51, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 115, 51, 51, 36, 36, 9, 1, 201, 201] 201 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]) total number of confs: 522 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045456 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CS1 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.2', 'C.2', 'S.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 55, 99, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 9, 55, 55, 99, 99, 195, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045456 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045456 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045456/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045456 Building REAL250005045457 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045457' /scratch/stefan/7916127/working/building/REAL250005045457 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045457 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045457/0 /scratch/stefan/7916127/working/building/REAL250005045457 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/587 `/scratch/stefan/7916127/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1(O)CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045457.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045457 none O=C(CC1(O)CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 180, 201, 201, 201, 201, 39, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 182, 182, 603, 201, 201, 201, 201, 201, 201, 107, 39, 39, 21, 21, 4, 1] 603 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: 1391 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: REAL250005045457 none O=C(CC1(O)CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [26, 6, 1, 1, 1, 1, 1, 1, 26, 26, 85, 116, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 26, 85, 85, 116, 116, 201, 201] 603 rigid atoms, others: [2, 3, 4, 5, 6, 7, 23, 24, 25, 26, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 749 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045457 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045457 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045457/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045457 Building REAL250005045458 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045458' /scratch/stefan/7916127/working/building/REAL250005045458 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045458 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045458/0 /scratch/stefan/7916127/working/building/REAL250005045458 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/588 `/scratch/stefan/7916127/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045458.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045458 none CC1=CNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 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, 80, 80, 80, 80, 37, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 79, 80, 37, 37, 24, 24, 9, 1] 80 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]) total number of confs: 263 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045458 none CC1=CNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 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, 4, 4, 4, 23, 36, 76, 76, 76, 80, 80, 80, 80, 80, 2, 2, 2, 1, 1, 4, 23, 23, 36, 36, 76, 80] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045458 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045458 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045458/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045458 Building REAL250005045459 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045459' /scratch/stefan/7916127/working/building/REAL250005045459 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045459 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045459/0 /scratch/stefan/7916127/working/building/REAL250005045459 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/589 `/scratch/stefan/7916127/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)=C1CCC1) `REAL250005045459.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045459 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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.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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 11, 11, 11, 63, 101, 197, 199, 197, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 11, 63, 63, 101, 101, 199, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 754 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: REAL250005045459 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)=C1CCC1 NO_LONG_NAME dock atom types: ['C.3', '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.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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 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, 4, 7, 6, 7, 7, 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, 118, 118, 118, 44, 28, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 118, 44, 44, 28, 28, 6, 1, 201, 201, 201, 201, 201, 201] 201 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: 656 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045459 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045459 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045459/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045459 Building REAL250005045460 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045460' /scratch/stefan/7916127/working/building/REAL250005045460 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045460 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045460/0 /scratch/stefan/7916127/working/building/REAL250005045460 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/590 `/scratch/stefan/7916127/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C#CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045460.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045460 none O=C(C#CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 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, 56, 56, 56, 56, 34, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 34, 34, 21, 21, 9, 1] 56 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]) 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: REAL250005045460 none O=C(C#CC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 50, 50, 50, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 50, 56] 56 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045460 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045460 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045460/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045460 Building REAL250005045461 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045461' /scratch/stefan/7916127/working/building/REAL250005045461 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045461 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045461/0 /scratch/stefan/7916127/working/building/REAL250005045461 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/591 `/scratch/stefan/7916127/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C#CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045461.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045461 none CC(C)(C)C#CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 59, 35, 22, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 35, 35, 22, 22, 7, 1] 59 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: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045461 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045461 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045461/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045461 Building REAL250005045462 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045462' /scratch/stefan/7916127/working/building/REAL250005045462 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045462 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045462/0 /scratch/stefan/7916127/working/building/REAL250005045462 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/592 `/scratch/stefan/7916127/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045462.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045462 none CC1=NN=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 55, 55, 55, 21, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 55, 21, 21, 12, 12, 4, 1, 118] 118 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]) total number of confs: 447 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045462 none CC1=NN=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 47, 65, 118, 118, 118, 118, 118, 118, 118, 118, 1, 2, 2, 2, 5, 5, 15, 47, 47, 65, 65, 118, 118, 1] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 20] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 438 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045462 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045462/1 /scratch/stefan/7916127/working/building/REAL250005045462 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/593 `/scratch/stefan/7916127/working/3D/593' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1) `REAL250005045462.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045462 none CC1=NC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 104, 54, 54, 54, 25, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 104, 104, 54, 25, 25, 16, 16, 4, 1, 201] 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]) total number of confs: 570 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045462 none CC1=NC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 48, 48, 48, 130, 155, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 8, 8, 48, 130, 130, 155, 155, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045462 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045462 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045462/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045462/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045462 Building REAL250005045463 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045463' /scratch/stefan/7916127/working/building/REAL250005045463 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045463 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045463/0 /scratch/stefan/7916127/working/building/REAL250005045463 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/594 `/scratch/stefan/7916127/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1) `REAL250005045463.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045463 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 88, 84, 84, 84, 43, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 84, 43, 43, 27, 27, 7, 1] 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]) 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: REAL250005045463 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 25, 45, 84, 84, 84, 88, 88, 88, 88, 88, 1, 1, 2, 2, 2, 1, 1, 7, 25, 25, 45, 45, 84, 88] 88 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 323 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045463 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045463 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045463/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045463 Building REAL250005045464 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045464' /scratch/stefan/7916127/working/building/REAL250005045464 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045464 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045464/0 /scratch/stefan/7916127/working/building/REAL250005045464 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/595 `/scratch/stefan/7916127/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])C1=CC(=O)[N-]O1) `REAL250005045464.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045464 none O=C(NCCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 19, 30, 93, 93, 93, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 5, 19, 19, 30, 30, 93, 201, 201, 1] 201 rigid atoms, others: [1, 16, 17, 18, 19, 20, 21, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045464 none O=C(NCCNC(=O)[C@@H]1C[C@H]1[N+](=O)[O-])C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 195, 98, 67, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 195, 201, 201, 201, 201, 201, 196, 98, 98, 67, 67, 12, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30]) total number of confs: 738 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045464 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045464 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045464/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045464 Building REAL250005045465 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045465' /scratch/stefan/7916127/working/building/REAL250005045465 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045465 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045465/0 /scratch/stefan/7916127/working/building/REAL250005045465 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/596 `/scratch/stefan/7916127/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN(C)N=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045465.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045465 none CC1=CN(C)N=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 83, 37, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 37, 37, 23, 23, 7, 1] 83 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: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045465 none CC1=CN(C)N=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 40, 81, 81, 81, 83, 83, 83, 83, 83, 2, 2, 2, 1, 2, 2, 2, 4, 22, 22, 40, 40, 81, 83] 83 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045465 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045465 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045465/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045465 Building REAL250005045466 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045466' /scratch/stefan/7916127/working/building/REAL250005045466 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045466 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045466/0 /scratch/stefan/7916127/working/building/REAL250005045466 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/597 `/scratch/stefan/7916127/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCC(F)C1)C1=CC(=O)[N-]O1) `REAL250005045466.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045466 none O=C(NCCNC(=O)C1CCCC(F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 45, 114, 114, 114, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 31, 31, 45, 45, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 37, 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]) total number of confs: 645 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045466 none O=C(NCCNC(=O)C1CCCC(F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 109, 72, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 195, 109, 109, 72, 72, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045466 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045466 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045466/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045466 Building REAL250005045467 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045467' /scratch/stefan/7916127/working/building/REAL250005045467 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045467 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045467/0 /scratch/stefan/7916127/working/building/REAL250005045467 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/598 `/scratch/stefan/7916127/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045467.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045467 none CN1C=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 138, 63, 63, 63, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 138, 138, 63, 25, 25, 14, 14, 4, 1] 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]) total number of confs: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045467 none CN1C=CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 87, 111, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 9, 9, 35, 87, 87, 111, 111, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045467 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045467 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045467/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045467 Building REAL250005045468 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045468' /scratch/stefan/7916127/working/building/REAL250005045468 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045468 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045468/0 /scratch/stefan/7916127/working/building/REAL250005045468 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/599 `/scratch/stefan/7916127/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045468.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045468 none COCC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 160, 96, 29, 29, 29, 24, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 160, 160, 201, 201, 201, 201, 201, 97, 97, 29, 24, 24, 15, 15, 4, 1, 160, 160, 160, 160] 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: 830 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: REAL250005045468 none COCC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 9, 1, 1, 1, 7, 37, 37, 37, 77, 81, 156, 156, 156, 160, 160, 160, 160, 160, 1, 1, 25, 25, 25, 9, 9, 7, 7, 37, 77, 77, 81, 81, 156, 160, 1, 1, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 37, 38, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 621 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045468 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045468 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045468/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045468 Building REAL250005045469 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045469' /scratch/stefan/7916127/working/building/REAL250005045469 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045469 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045469/0 /scratch/stefan/7916127/working/building/REAL250005045469 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/600 `/scratch/stefan/7916127/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045469.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045469 none COCCC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens need 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, 187, 100, 100, 100, 35, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 198, 198, 187, 187, 100, 35, 35, 22, 22, 4, 1] 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]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045469 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045469 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045469/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045469 Building REAL250005045470 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045470' /scratch/stefan/7916127/working/building/REAL250005045470 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045470 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045470/0 /scratch/stefan/7916127/working/building/REAL250005045470 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/601 `/scratch/stefan/7916127/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC1)C1=CC(=O)[N-]O1) `REAL250005045470.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045470 none O=C(NCCNC(=O)C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 48, 103, 103, 103, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 30, 30, 48, 48, 103, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 659 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: REAL250005045470 none O=C(NCCNC(=O)C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 183, 95, 55, 13, 13, 1, 13, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201, 185, 95, 95, 55, 55, 13, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31]) total number of confs: 697 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045470 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045470 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045470/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045470 Building REAL250005045471 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045471' /scratch/stefan/7916127/working/building/REAL250005045471 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045471 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045471/0 /scratch/stefan/7916127/working/building/REAL250005045471 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/602 `/scratch/stefan/7916127/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCC1)C1=CC(=O)[N-]O1) `REAL250005045471.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045471 none O=C(NCCNC(=O)C1CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 33, 50, 115, 115, 115, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 33, 33, 50, 50, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 652 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: REAL250005045471 none O=C(NCCNC(=O)C1CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 100, 54, 10, 10, 1, 10, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 187, 100, 100, 54, 54, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 717 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045471 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045471 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045471/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045471 Building REAL250005045472 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045472' /scratch/stefan/7916127/working/building/REAL250005045472 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045472 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045472/0 /scratch/stefan/7916127/working/building/REAL250005045472 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/603 `/scratch/stefan/7916127/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCOCC1)C1=CC(=O)[N-]O1) `REAL250005045472.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045472 none O=C(NCCNC(=O)C1CCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 46, 129, 129, 129, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 32, 32, 46, 46, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 637 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045472 none O=C(NCCNC(=O)C1CCOCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 189, 115, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 191, 201, 201, 201, 201, 201, 191, 115, 115, 69, 69, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045472 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045472 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045472/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045472 Building REAL250005045473 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045473' /scratch/stefan/7916127/working/building/REAL250005045473 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045473 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045473/0 /scratch/stefan/7916127/working/building/REAL250005045473 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/604 `/scratch/stefan/7916127/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(=O)N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045473.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045473 none O=C(CC1CCC(=O)N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', '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: [11, 1, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 170, 201, 201, 201, 201, 201, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 201, 87, 33, 33, 20, 20, 4, 1] 201 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: 793 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045473 none O=C(CC1CCC(=O)N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', '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: [11, 1, 5, 5, 5, 5, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31, 102, 128, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 31, 102, 102, 128, 128, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 743 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045473 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045473 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045473/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045473 Building REAL250005045474 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045474' /scratch/stefan/7916127/working/building/REAL250005045474 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045474 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045474/0 /scratch/stefan/7916127/working/building/REAL250005045474 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/605 `/scratch/stefan/7916127/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045474.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045474 none CNC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 178, 201, 78, 78, 78, 20, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 178, 178, 201, 201, 201, 201, 78, 20, 20, 12, 12, 4, 1, 178, 178, 178, 178] 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: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045474 none CNC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 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] 0 hydrogens 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, 5, 1, 5, 1, 1, 7, 7, 7, 49, 73, 173, 177, 177, 178, 178, 178, 178, 178, 1, 1, 5, 5, 5, 5, 7, 49, 49, 73, 73, 177, 178, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 4, 5, 34, 19, 20] set([0, 1, 3, 6, 7, 8, 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: 616 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045474 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045474 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045474/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045474 Building REAL250005045475 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045475' /scratch/stefan/7916127/working/building/REAL250005045475 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045475 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045475/0 /scratch/stefan/7916127/working/building/REAL250005045475 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/606 `/scratch/stefan/7916127/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045475.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045475 none CN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 69, 69, 69, 41, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 69, 41, 41, 26, 26, 9, 1] 71 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]) total number of confs: 262 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045475 none CN1N=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 36, 64, 64, 64, 71, 71, 71, 71, 71, 1, 2, 2, 2, 1, 4, 23, 23, 36, 36, 64, 71] 71 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045475 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045475 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045475/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045475 Building REAL250005045476 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045476' /scratch/stefan/7916127/working/building/REAL250005045476 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045476 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045476/0 /scratch/stefan/7916127/working/building/REAL250005045476 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/607 `/scratch/stefan/7916127/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CS1) `REAL250005045476.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045476 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 84, 84, 84, 44, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 161, 161, 161, 161, 161, 161, 84, 44, 44, 30, 30, 11, 1, 161] 161 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]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045476 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 31, 65, 149, 149, 149, 161, 161, 161, 161, 161, 1, 1, 2, 2, 2, 1, 5, 31, 31, 65, 65, 149, 161, 1] 161 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045476 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045476 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045476/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045476 Building REAL250005045477 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045477' /scratch/stefan/7916127/working/building/REAL250005045477 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045477 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045477/0 /scratch/stefan/7916127/working/building/REAL250005045477 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/608 `/scratch/stefan/7916127/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCOCC1) `REAL250005045477.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045477 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCOCC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 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, 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: [155, 114, 114, 114, 48, 33, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155, 114, 48, 48, 33, 33, 13, 1, 155, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 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: 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: REAL250005045477 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCOCC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 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, 7, 7] 0 hydrogens need rotated 155 conformations in input total number of sets (complete confs): 155 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 4, 4, 21, 41, 135, 135, 135, 155, 155, 155, 155, 155, 1, 1, 1, 1, 1, 2, 2, 2, 4, 21, 21, 41, 41, 135, 155, 1, 1, 1, 1, 1, 1, 1, 1] 155 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 16, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 473 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045477 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045477 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045477/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045477 Building REAL250005045478 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045478' /scratch/stefan/7916127/working/building/REAL250005045478 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045478 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045478/0 /scratch/stefan/7916127/working/building/REAL250005045478 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/609 `/scratch/stefan/7916127/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045478.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045478 none CC(C)CC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 199, 148, 200, 37, 37, 37, 24, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148, 37, 24, 24, 15, 15, 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: 865 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045478 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045478 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045478/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045478 Building REAL250005045479 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045479' /scratch/stefan/7916127/working/building/REAL250005045479 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045479 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045479/0 /scratch/stefan/7916127/working/building/REAL250005045479 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/610 `/scratch/stefan/7916127/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045479.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045479 none CC1=NN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 174, 174, 174, 102, 102, 102, 43, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 102, 43, 43, 32, 32, 11, 1] 174 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: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045479 none CC1=NN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 4, 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 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 55, 89, 168, 168, 168, 174, 174, 174, 174, 174, 2, 2, 2, 1, 1, 10, 55, 55, 89, 89, 168, 174] 174 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 650 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045479 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045479 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045479/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045479 Building REAL250005045480 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045480' /scratch/stefan/7916127/working/building/REAL250005045480 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045480 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045480/0 /scratch/stefan/7916127/working/building/REAL250005045480 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/611 `/scratch/stefan/7916127/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045480.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045480 none C[N@@H+]1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 13, 10, 10, 10, 10, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 10, 10, 10, 7, 7, 3, 1, 14, 14] 14 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, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045480 none C[N@@H+]1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 14, 14, 1, 1] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045480 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045480/1 /scratch/stefan/7916127/working/building/REAL250005045480 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/612 `/scratch/stefan/7916127/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045480.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045480/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045480 none C[N@H+]1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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, 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, 11, 11, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 3, 1, 11, 11] 11 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, 39, 40]) total number of confs: 40 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045480 none C[N@H+]1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 6, 8, 8, 8, 8, 11, 11, 1, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045480 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045480 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045480/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045480/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045480 Building REAL250005045481 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045481' /scratch/stefan/7916127/working/building/REAL250005045481 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045481 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045481/0 /scratch/stefan/7916127/working/building/REAL250005045481 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/613 `/scratch/stefan/7916127/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045481.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045481 none CN1C=NC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 177, 81, 81, 81, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 177, 177, 81, 23, 23, 14, 14, 4, 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: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045481 none CN1C=NC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 29, 89, 110, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 5, 5, 29, 89, 89, 110, 110, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([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]) total number of confs: 728 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045481 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045481 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045481/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045481 Building REAL250005045482 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045482' /scratch/stefan/7916127/working/building/REAL250005045482 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045482 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045482/0 /scratch/stefan/7916127/working/building/REAL250005045482 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/614 `/scratch/stefan/7916127/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045482.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045482 none CCN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 127, 127, 127, 127, 121, 121, 121, 47, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 127, 182, 182, 182, 182, 182, 127, 121, 47, 47, 29, 29, 7, 1, 127] 182 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]) total number of confs: 738 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045482 none CCN1C=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'N.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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 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: [7, 1, 1, 1, 1, 1, 1, 5, 5, 4, 25, 42, 113, 113, 113, 127, 127, 127, 127, 127, 1, 7, 7, 7, 7, 7, 1, 5, 25, 25, 42, 42, 113, 127, 1] 182 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 425 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045482 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045482 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045482/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045482 Building REAL250005045483 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045483' /scratch/stefan/7916127/working/building/REAL250005045483 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045483 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045483/0 /scratch/stefan/7916127/working/building/REAL250005045483 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/615 `/scratch/stefan/7916127/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005045483.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045483 none CCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C 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', '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'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 17, 17, 17, 15, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 15, 15, 13, 13, 4, 1, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045483 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045483 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045483/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045483 Building REAL250005045484 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045484' /scratch/stefan/7916127/working/building/REAL250005045484 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045484 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045484/0 /scratch/stefan/7916127/working/building/REAL250005045484 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/616 `/scratch/stefan/7916127/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C(C)O1) `REAL250005045484.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045484 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C(C)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 123, 123, 49, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 49, 49, 29, 29, 8, 1, 201, 201, 201, 201] 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]) total number of confs: 654 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045484 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C(C)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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 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, 10, 10, 10, 56, 88, 196, 197, 196, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 56, 56, 88, 88, 197, 201, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38]) total number of confs: 721 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045484 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045484 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045484/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045484 Building REAL250005045485 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045485' /scratch/stefan/7916127/working/building/REAL250005045485 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045485 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045485/0 /scratch/stefan/7916127/working/building/REAL250005045485 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/617 `/scratch/stefan/7916127/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045485.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045485 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', '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, 7, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 91, 201, 91, 91, 34, 23, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 34, 34, 23, 23, 5, 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: 604 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045485 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', '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, 7, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 1, 1, 12, 12, 12, 66, 104, 196, 199, 196, 201, 201, 201, 201, 201, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 12, 66, 66, 104, 104, 199, 201] 201 rigid atoms, others: [32, 1, 4, 5, 6, 7, 8, 9, 33] set([0, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 755 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045485 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045485 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045485/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045485 Building REAL250005045486 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045486' /scratch/stefan/7916127/working/building/REAL250005045486 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045486 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045486/0 /scratch/stefan/7916127/working/building/REAL250005045486 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/618 `/scratch/stefan/7916127/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045486.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045486 none CC1CC1C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 12, 12, 12, 61, 74, 158, 162, 158, 167, 167, 167, 167, 167, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 12, 61, 61, 74, 74, 162, 167] 201 rigid atoms, others: [3, 4, 5, 6, 7, 28, 29, 30, 31] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 587 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045486 none CC1CC1C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 167, 167, 167, 58, 58, 58, 24, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 167, 167, 167, 167, 58, 24, 24, 16, 16, 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: 613 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045486 none CC1CC1C1CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 32, 32, 32, 103, 120, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5, 32, 103, 103, 120, 120, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045486 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045486 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045486/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045486 Building REAL250005045487 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045487' /scratch/stefan/7916127/working/building/REAL250005045487 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045487 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045487/0 /scratch/stefan/7916127/working/building/REAL250005045487 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/619 `/scratch/stefan/7916127/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@@H]1C[C@H]1C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045487.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045487 none O=C(C[C@@H]1C[C@H]1C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 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, 7] 0 hydrogens 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, 27, 6, 6, 6, 6, 1, 6, 1, 1, 1, 100, 100, 140, 141, 201, 201, 201, 201, 201, 201, 201, 201, 27, 27, 6, 6, 1, 1, 1, 1, 1, 100, 140, 140, 141, 141, 201, 201] 201 rigid atoms, others: [6, 8, 9, 10, 27, 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, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 704 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045487 none O=C(C[C@@H]1C[C@H]1C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 107, 180, 180, 180, 180, 180, 201, 201, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 107, 107, 180, 180, 201, 201, 201, 201, 201, 32, 21, 21, 14, 14, 4, 1] 201 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: 757 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045487 none O=C(C[C@@H]1C[C@H]1C1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 7, 1, 1, 1, 1, 1, 1, 1, 6, 6, 49, 49, 100, 101, 177, 177, 177, 180, 180, 180, 180, 180, 7, 7, 1, 1, 6, 6, 6, 6, 6, 49, 100, 100, 101, 101, 177, 180] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045487 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045487 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045487/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045487 Building REAL250005045488 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045488' /scratch/stefan/7916127/working/building/REAL250005045488 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045488 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045488/0 /scratch/stefan/7916127/working/building/REAL250005045488 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/620 `/scratch/stefan/7916127/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045488.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045488 none CC1COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [152, 152, 152, 152, 113, 113, 113, 53, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 152, 152, 152, 152, 152, 152, 152, 152, 113, 53, 53, 32, 32, 9, 1, 152, 152] 152 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: 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: REAL250005045488 none CC1COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 53, 94, 147, 150, 150, 152, 152, 152, 152, 152, 1, 2, 2, 2, 1, 1, 1, 1, 11, 53, 53, 94, 94, 150, 152, 1, 1] 152 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 23, 24, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045488 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045488 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045488/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045488 Building REAL250005045489 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045489' /scratch/stefan/7916127/working/building/REAL250005045489 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045489 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045489/0 /scratch/stefan/7916127/working/building/REAL250005045489 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/621 `/scratch/stefan/7916127/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]12C[C@H]1CCC2)C1=CC(=O)[N-]O1) `REAL250005045489.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045489 none O=C(NCCNC(=O)[C@]12C[C@H]1CCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens 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, 31, 50, 103, 103, 103, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 30, 30, 50, 50, 103, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 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]) total number of confs: 520 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: REAL250005045489 none O=C(NCCNC(=O)[C@]12C[C@H]1CCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens 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, 191, 85, 47, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 191, 201, 201, 201, 201, 201, 192, 85, 85, 47, 47, 6, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 706 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045489 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045489 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045489/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045489 Building REAL250005045490 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045490' /scratch/stefan/7916127/working/building/REAL250005045490 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045490 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045490/0 /scratch/stefan/7916127/working/building/REAL250005045490 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/622 `/scratch/stefan/7916127/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1OCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045490.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045490 none CC[C@@H]1OCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 194, 194, 194, 194, 194, 103, 194, 103, 103, 36, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 194, 194, 103, 36, 36, 26, 26, 7, 1] 201 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: 638 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: REAL250005045490 none CC[C@@H]1OCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 84, 188, 188, 188, 194, 194, 194, 194, 194, 4, 4, 4, 4, 4, 1, 1, 1, 1, 11, 58, 58, 84, 84, 188, 194] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 679 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045490 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045490 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045490/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045490 Building REAL250005045491 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045491' /scratch/stefan/7916127/working/building/REAL250005045491 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045491 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045491/0 /scratch/stefan/7916127/working/building/REAL250005045491 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/623 `/scratch/stefan/7916127/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1) `REAL250005045491.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045491 none CCC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 142, 142, 142, 126, 126, 126, 44, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 142, 142, 201, 201, 201, 201, 201, 142, 126, 44, 44, 26, 26, 5, 1] 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]) total number of confs: 777 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045491 none CCC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 1, 1, 1, 1, 7, 7, 7, 29, 52, 130, 130, 130, 142, 142, 142, 142, 142, 1, 1, 8, 9, 9, 8, 8, 1, 7, 29, 29, 52, 52, 130, 142] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 486 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045491 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045491 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045491/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045491 Building REAL250005045492 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045492' /scratch/stefan/7916127/working/building/REAL250005045492 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045492 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045492/0 /scratch/stefan/7916127/working/building/REAL250005045492 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/624 `/scratch/stefan/7916127/working/3D/624' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005045492.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045492 none CCC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 190, 135, 31, 31, 31, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 182, 198, 198, 200, 200, 200, 199, 200, 192, 135, 135, 31, 25, 25, 16, 16, 4, 1, 198, 198, 198, 198, 198, 198, 198] 201 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, 39, 40, 41, 42]) total number of confs: 964 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045492 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045492 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045492/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045492 Building REAL250005045493 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045493' /scratch/stefan/7916127/working/building/REAL250005045493 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045493 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045493/0 /scratch/stefan/7916127/working/building/REAL250005045493 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/625 `/scratch/stefan/7916127/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045493.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045493 none C[NH+](C)CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 65, 69, 37, 37, 37, 21, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 68, 68, 71, 71, 69, 69, 37, 21, 21, 16, 16, 4, 1] 71 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: 330 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045493 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045493 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045493/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045493 Building REAL250005045494 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045494' /scratch/stefan/7916127/working/building/REAL250005045494 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045494 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045494/0 /scratch/stefan/7916127/working/building/REAL250005045494 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/626 `/scratch/stefan/7916127/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CCC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045494.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045494 none O=C(NCCNC(=O)[C@@H]1CCC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 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: [10, 1, 10, 10, 33, 46, 103, 103, 103, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 10, 33, 33, 46, 46, 103, 161, 161, 161, 161, 161, 1] 161 rigid atoms, others: [32, 1, 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]) total number of confs: 526 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: REAL250005045494 none O=C(NCCNC(=O)[C@@H]1CCC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 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: [152, 151, 89, 65, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 152, 161, 161, 161, 161, 161, 152, 89, 89, 65, 65, 12, 1, 1, 1, 1, 1, 161] 161 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 594 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045494 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045494 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045494/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045494 Building REAL250005045495 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045495' /scratch/stefan/7916127/working/building/REAL250005045495 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045495 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045495/0 /scratch/stefan/7916127/working/building/REAL250005045495 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/627 `/scratch/stefan/7916127/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CC[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045495.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045495 none C[C@H]1CC[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 5, 5, 7, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 123, 201, 123, 123, 50, 34, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 50, 50, 34, 34, 7, 1, 201, 201, 201, 201] 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, 37, 38, 39, 40]) total number of confs: 639 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045495 none C[C@H]1CC[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 5, 5, 7, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 65, 111, 191, 193, 191, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 12, 65, 65, 111, 111, 193, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 38, 39, 40, 21, 22, 26, 27, 28, 29, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 758 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045495 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045495 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045495/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045495 Building REAL250005045496 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045496' /scratch/stefan/7916127/working/building/REAL250005045496 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045496 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045496/0 /scratch/stefan/7916127/working/building/REAL250005045496 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/628 `/scratch/stefan/7916127/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005045496.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045496 none CC(C)C(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 11, 11, 11, 11, 10, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 10, 10, 3, 1, 12, 12, 12, 12, 12, 12] 12 rigid atoms, others: [36, 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, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 47 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045496 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045496 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045496/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045496 Building REAL250005045497 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045497' /scratch/stefan/7916127/working/building/REAL250005045497 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045497 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045497/0 /scratch/stefan/7916127/working/building/REAL250005045497 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/629 `/scratch/stefan/7916127/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045497.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045497 none CCC[N@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 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, 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, 18, 18, 18, 18, 18, 18, 14, 14, 14, 12, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 12, 12, 11, 11, 4, 1] 19 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: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045497 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045497/1 /scratch/stefan/7916127/working/building/REAL250005045497 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/630 `/scratch/stefan/7916127/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045497.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005045497 none CCC[N@@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 7, 6, 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, 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, 18, 18, 18, 18, 18, 18, 14, 14, 14, 12, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 14, 12, 12, 11, 11, 4, 1] 19 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: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045497 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045497 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045497/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045497/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045497 Building REAL250005045498 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045498' /scratch/stefan/7916127/working/building/REAL250005045498 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045498 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045498/0 /scratch/stefan/7916127/working/building/REAL250005045498 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/631 `/scratch/stefan/7916127/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@H+](C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045498.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045498 none CCC[N@H+](C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 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, 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, 85, 74, 58, 74, 74, 44, 44, 44, 17, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 85, 85, 74, 74, 74, 58, 58, 44, 17, 17, 14, 14, 4, 1] 113 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: 532 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045498 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045498/1 /scratch/stefan/7916127/working/building/REAL250005045498 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/632 `/scratch/stefan/7916127/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[N@@H+](C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045498.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005045498 none CCC[N@@H+](C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 9, 6, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 6, 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, 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, 85, 74, 58, 74, 74, 44, 44, 44, 17, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 85, 85, 74, 74, 74, 58, 58, 44, 17, 17, 14, 14, 4, 1] 113 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: 532 number of broken/clashed sets: 89 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045498 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045498 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045498/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045498/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045498 Building REAL250005045499 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045499' /scratch/stefan/7916127/working/building/REAL250005045499 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045499 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045499/0 /scratch/stefan/7916127/working/building/REAL250005045499 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/633 `/scratch/stefan/7916127/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)C) `REAL250005045499.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045499 none CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)C 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', '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, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [155, 153, 72, 72, 72, 46, 32, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 155, 155, 155, 155, 155, 155, 155, 155, 153, 153, 72, 46, 46, 32, 32, 9, 1, 155, 155, 155, 155, 155, 155, 155, 155, 155] 155 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 643 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045499 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045499 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045499/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045499 Building REAL250005045500 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045500' /scratch/stefan/7916127/working/building/REAL250005045500 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045500 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045500/0 /scratch/stefan/7916127/working/building/REAL250005045500 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/634 `/scratch/stefan/7916127/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1) `REAL250005045500.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045500 none CC1=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 66, 66, 66, 25, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 163, 163, 66, 25, 25, 14, 14, 4, 1, 201, 201] 201 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: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045500 none CC1=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 35, 35, 35, 91, 103, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 6, 6, 35, 91, 91, 103, 103, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045500 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045500 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045500/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045500 Building REAL250005045501 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045501' /scratch/stefan/7916127/working/building/REAL250005045501 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045501 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045501/0 /scratch/stefan/7916127/working/building/REAL250005045501 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/635 `/scratch/stefan/7916127/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1) `REAL250005045501.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045501 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 178, 96, 96, 96, 46, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 178, 178, 178, 201, 201, 201, 201, 201, 96, 46, 46, 31, 31, 11, 1, 178, 178] 201 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: 596 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: REAL250005045501 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 11, 11, 55, 75, 158, 158, 158, 178, 178, 178, 178, 178, 1, 1, 1, 6, 6, 6, 5, 5, 11, 55, 55, 75, 75, 158, 178, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 34, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 606 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045501 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045501 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045501/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045501 Building REAL250005045502 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045502' /scratch/stefan/7916127/working/building/REAL250005045502 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045502 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045502/0 /scratch/stefan/7916127/working/building/REAL250005045502 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/636 `/scratch/stefan/7916127/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045502.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045502 none CC1=NNC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 119, 119, 119, 119, 110, 110, 110, 40, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 119, 119, 110, 40, 40, 27, 27, 8, 1] 119 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: 357 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: REAL250005045502 none CC1=NNC(C)=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 34, 52, 118, 118, 118, 120, 120, 120, 120, 120, 2, 2, 2, 1, 2, 2, 2, 8, 34, 34, 52, 52, 118, 120] 120 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 428 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045502 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045502 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045502/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045502 Building REAL250005045503 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045503' /scratch/stefan/7916127/working/building/REAL250005045503 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045503 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045503/0 /scratch/stefan/7916127/working/building/REAL250005045503 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/637 `/scratch/stefan/7916127/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045503.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045503 none CC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 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: [193, 193, 193, 193, 193, 193, 123, 123, 123, 53, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 123, 53, 53, 36, 36, 10, 1] 193 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]) total number of confs: 521 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045503 none CC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 65, 114, 186, 187, 186, 193, 193, 193, 193, 193, 2, 2, 2, 1, 1, 1, 10, 65, 65, 114, 114, 187, 193] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045503 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045503 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045503/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045503 Building REAL250005045504 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045504' /scratch/stefan/7916127/working/building/REAL250005045504 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045504 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045504/0 /scratch/stefan/7916127/working/building/REAL250005045504 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/638 `/scratch/stefan/7916127/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045504.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045504 none CC(C)CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 171, 193, 179, 136, 133, 42, 42, 42, 26, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 191, 201, 201, 193, 201, 194, 194, 175, 176, 160, 160, 134, 134, 42, 26, 26, 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: 1253 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045504 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045504 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045504/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045504 Building REAL250005045505 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045505' /scratch/stefan/7916127/working/building/REAL250005045505 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045505 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045505/0 /scratch/stefan/7916127/working/building/REAL250005045505 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/639 `/scratch/stefan/7916127/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045505.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045505 none CC(C)(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 201, 200, 115, 115, 115, 51, 32, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 51, 51, 32, 32, 7, 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: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045505 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045505 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045505/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045505 Building REAL250005045506 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045506' /scratch/stefan/7916127/working/building/REAL250005045506 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045506 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045506/0 /scratch/stefan/7916127/working/building/REAL250005045506 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/640 `/scratch/stefan/7916127/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=NC=N1)C1=CC(=O)[N-]O1) `REAL250005045506.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045506 none O=C(NCCNC(=O)C1=CC=NC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 3, 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: [5, 1, 5, 5, 14, 19, 41, 41, 41, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 5, 14, 14, 19, 19, 41, 65, 65, 65, 1] 65 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL250005045506 none O=C(NCCNC(=O)C1=CC=NC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 3, 7, 3, 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: [63, 63, 45, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 63, 65, 65, 65, 65, 65, 63, 45, 45, 36, 36, 12, 1, 1, 1, 65] 65 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045506 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045506 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045506/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045506 Building REAL250005045507 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045507' /scratch/stefan/7916127/working/building/REAL250005045507 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045507 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045507/0 /scratch/stefan/7916127/working/building/REAL250005045507 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/641 `/scratch/stefan/7916127/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC=N1) `REAL250005045507.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045507 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [171, 171, 171, 81, 81, 81, 48, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 171, 171, 131, 171, 171, 171, 171, 81, 48, 48, 34, 34, 11, 1, 171, 171] 171 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]) total number of confs: 537 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045507 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 35, 73, 159, 159, 159, 171, 171, 171, 171, 171, 1, 1, 1, 2, 2, 2, 1, 7, 35, 35, 73, 73, 159, 171, 1, 1] 171 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045507 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045507 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045507/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045507 Building REAL250005045508 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045508' /scratch/stefan/7916127/working/building/REAL250005045508 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045508 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045508/0 /scratch/stefan/7916127/working/building/REAL250005045508 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/642 `/scratch/stefan/7916127/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045508.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045508 none O=C(CC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 143, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 143, 143, 201, 201, 201, 60, 23, 23, 14, 14, 4, 1] 201 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]) total number of confs: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045508 none O=C(CC1=CC=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 5, 1, 1, 1, 1, 1, 1, 29, 29, 121, 145, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 29, 121, 121, 145, 145, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045508 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045508 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045508/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045508 Building REAL250005045509 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045509' /scratch/stefan/7916127/working/building/REAL250005045509 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045509 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045509/0 /scratch/stefan/7916127/working/building/REAL250005045509 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/643 `/scratch/stefan/7916127/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC=CC=N1)C1=CC(=O)[N-]O1) `REAL250005045509.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045509 none O=C(NCCNC(=O)C1=NC=CC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 22, 34, 71, 71, 71, 79, 79, 71, 79, 79, 1, 1, 1, 1, 1, 1, 9, 22, 22, 34, 34, 71, 79, 71, 79, 1] 79 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL250005045509 none O=C(NCCNC(=O)C1=NC=CC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [39, 39, 29, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 39, 41, 41, 41, 41, 41, 39, 29, 29, 22, 22, 8, 1, 1, 1, 41] 41 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045509 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045509 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045509/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045509 Building REAL250005045510 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045510' /scratch/stefan/7916127/working/building/REAL250005045510 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045510 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045510/0 /scratch/stefan/7916127/working/building/REAL250005045510 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/644 `/scratch/stefan/7916127/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045510.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045510 none CCC(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 125, 197, 112, 35, 35, 35, 25, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 197, 197, 197, 143, 143, 112, 112, 35, 25, 25, 16, 16, 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: 998 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045510 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045510 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045510/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045510 Building REAL250005045511 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045511' /scratch/stefan/7916127/working/building/REAL250005045511 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045511 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045511/0 /scratch/stefan/7916127/working/building/REAL250005045511 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/645 `/scratch/stefan/7916127/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CN=N1)C1=CC(=O)[N-]O1) `REAL250005045511.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045511 none O=C(NCCNC(=O)C1=CC=CN=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 21, 26, 49, 49, 49, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 8, 21, 21, 26, 26, 49, 84, 84, 84, 1] 84 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 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: REAL250005045511 none O=C(NCCNC(=O)C1=CC=CN=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 50, 38, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 82, 84, 84, 84, 84, 84, 82, 50, 50, 38, 38, 12, 1, 1, 1, 84] 84 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29]) total number of confs: 307 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045511 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045511 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045511/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045511 Building REAL250005045512 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045512' /scratch/stefan/7916127/working/building/REAL250005045512 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045512 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045512/0 /scratch/stefan/7916127/working/building/REAL250005045512 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/646 `/scratch/stefan/7916127/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045512.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045512 none COC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 120, 120, 120, 120, 92, 92, 92, 44, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 120, 132, 132, 132, 120, 120, 92, 44, 44, 26, 26, 7, 1] 132 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]) 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: REAL250005045512 none COC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', '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', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 33, 52, 112, 112, 112, 120, 120, 120, 120, 120, 1, 5, 5, 5, 1, 1, 10, 33, 33, 52, 52, 112, 120] 132 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 24, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045512 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045512 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045512/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045512 Building REAL250005045513 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045513' /scratch/stefan/7916127/working/building/REAL250005045513 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045513 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045513/0 /scratch/stefan/7916127/working/building/REAL250005045513 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/647 `/scratch/stefan/7916127/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)O1) `REAL250005045513.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045513 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 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, 90, 90, 90, 90, 90, 43, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 43, 43, 29, 29, 7, 1, 90, 90, 90] 90 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: 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: REAL250005045513 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 24, 43, 88, 88, 88, 90, 90, 90, 90, 90, 1, 1, 1, 2, 2, 2, 4, 24, 24, 43, 43, 88, 90, 2, 2, 2] 90 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 336 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045513 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045513 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045513/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045513 Building REAL250005045514 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045514' /scratch/stefan/7916127/working/building/REAL250005045514 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045514 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045514/0 /scratch/stefan/7916127/working/building/REAL250005045514 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/648 `/scratch/stefan/7916127/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=NN=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045514.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045514 none O=C(CCN1C=NN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 131, 156, 201, 201, 201, 201, 29, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 131, 131, 156, 156, 201, 72, 29, 29, 20, 20, 6, 1] 201 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: 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: REAL250005045514 none O=C(CCN1C=NN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 17, 9, 1, 1, 1, 1, 1, 1, 75, 75, 127, 154, 199, 199, 199, 201, 201, 201, 201, 201, 17, 17, 9, 9, 1, 75, 129, 129, 153, 153, 199, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 756 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045514 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045514 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045514/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045514 Building REAL250005045515 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045515' /scratch/stefan/7916127/working/building/REAL250005045515 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045515 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045515/0 /scratch/stefan/7916127/working/building/REAL250005045515 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/649 `/scratch/stefan/7916127/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=NC=CC=C1F)C1=CC(=O)[N-]O1) `REAL250005045515.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045515 none O=C(NCCNC(=O)C1=NC=CC=C1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 24, 35, 91, 91, 91, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 7, 24, 24, 35, 35, 91, 133, 133, 133, 1] 133 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 360 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045515 none O=C(NCCNC(=O)C1=NC=CC=C1F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [131, 131, 79, 56, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 131, 133, 133, 133, 133, 133, 131, 79, 79, 56, 56, 12, 1, 1, 1, 133] 133 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045515 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045515 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045515/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045515 Building REAL250005045516 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045516' /scratch/stefan/7916127/working/building/REAL250005045516 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045516 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045516/0 /scratch/stefan/7916127/working/building/REAL250005045516 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/650 `/scratch/stefan/7916127/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1OCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045516.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045516 none CC1OCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 69, 69, 69, 39, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 69, 39, 39, 28, 28, 9, 1] 82 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: 293 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: REAL250005045516 none CC1OCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 17, 31, 76, 76, 76, 82, 82, 82, 82, 82, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 17, 17, 31, 31, 76, 82] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 284 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045516 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045516 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045516/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045516 Building REAL250005045517 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045517' /scratch/stefan/7916127/working/building/REAL250005045517 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045517 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045517/0 /scratch/stefan/7916127/working/building/REAL250005045517 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/651 `/scratch/stefan/7916127/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCOC1) `REAL250005045517.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045517 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCOC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 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, 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] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 99, 99, 99, 50, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 177, 99, 50, 50, 33, 33, 10, 1, 177, 177, 177, 177, 177, 177] 177 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: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045517 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCOC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 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, 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] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 5, 35, 70, 168, 168, 168, 177, 177, 177, 177, 177, 1, 1, 1, 1, 2, 2, 2, 5, 35, 35, 70, 70, 168, 177, 1, 1, 1, 1, 1, 1] 177 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 618 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045517 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045517 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045517/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045517 Building REAL250005045518 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045518' /scratch/stefan/7916127/working/building/REAL250005045518 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045518 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045518/0 /scratch/stefan/7916127/working/building/REAL250005045518 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/652 `/scratch/stefan/7916127/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045518.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045518 none CCC(CC)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [145, 122, 61, 122, 143, 123, 99, 61, 61, 29, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 146, 146, 146, 146, 145, 145, 145, 146, 146, 145, 125, 125, 125, 125, 125, 61, 29, 29, 20, 20, 4, 1] 148 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: 999 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045518 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045518 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045518/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045518 Building REAL250005045519 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045519' /scratch/stefan/7916127/working/building/REAL250005045519 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045519 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045519/0 /scratch/stefan/7916127/working/building/REAL250005045519 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/653 `/scratch/stefan/7916127/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCO1) `REAL250005045519.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045519 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 125, 125, 125, 51, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 180, 180, 180, 125, 51, 51, 36, 36, 10, 1, 180, 180, 180, 180] 180 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]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045519 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCO1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 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, 6, 6, 6, 37, 70, 165, 165, 165, 180, 180, 180, 180, 180, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 6, 37, 37, 70, 70, 165, 180, 1, 1, 1, 1] 180 rigid atoms, others: [0, 1, 2, 3, 4, 37, 35, 38, 18, 19, 20, 24, 25, 26, 27, 36] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045519 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045519 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045519/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045519 Building REAL250005045520 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045520' /scratch/stefan/7916127/working/building/REAL250005045520 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045520 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045520/0 /scratch/stefan/7916127/working/building/REAL250005045520 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/654 `/scratch/stefan/7916127/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045520.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045520 none CCCC(C)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 195, 144, 82, 145, 146, 168, 82, 82, 27, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 198, 198, 198, 198, 198, 198, 197, 147, 147, 145, 170, 170, 170, 170, 170, 82, 27, 27, 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: 1055 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045520 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045520 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045520/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045520 Building REAL250005045521 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045521' /scratch/stefan/7916127/working/building/REAL250005045521 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045521 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045521/0 /scratch/stefan/7916127/working/building/REAL250005045521 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/655 `/scratch/stefan/7916127/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045521.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045521 none CCC(CC)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 171, 135, 172, 194, 30, 30, 30, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 194, 194, 192, 194, 174, 194, 193, 194, 194, 194, 135, 135, 30, 23, 23, 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: 987 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045521 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045521 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045521/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045521 Building REAL250005045522 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045522' /scratch/stefan/7916127/working/building/REAL250005045522 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045522 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045522/0 /scratch/stefan/7916127/working/building/REAL250005045522 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/656 `/scratch/stefan/7916127/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045522.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045522 none CCC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 154, 180, 72, 154, 72, 72, 36, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 181, 181, 181, 181, 154, 154, 154, 154, 72, 36, 36, 21, 21, 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: 879 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045522 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045522 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045522/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045522 Building REAL250005045523 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045523' /scratch/stefan/7916127/working/building/REAL250005045523 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045523 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045523/0 /scratch/stefan/7916127/working/building/REAL250005045523 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/657 `/scratch/stefan/7916127/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045523.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045523 none CCCC(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 167, 122, 50, 122, 137, 50, 50, 30, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 188, 188, 188, 188, 188, 167, 167, 122, 151, 151, 151, 151, 151, 50, 30, 30, 20, 20, 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: 1114 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045523 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045523 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045523/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045523 Building REAL250005045524 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045524' /scratch/stefan/7916127/working/building/REAL250005045524 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045524 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045524/0 /scratch/stefan/7916127/working/building/REAL250005045524 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/658 `/scratch/stefan/7916127/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)NCC1CC1) `REAL250005045524.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045524 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [40, 29, 40, 40, 92, 133, 201, 201, 201, 201, 201, 201, 201, 201, 29, 29, 8, 1, 1, 1, 1, 40, 92, 92, 133, 133, 201, 201, 29, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045524 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)NCC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 30, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 79, 95, 95, 95, 147, 201, 201, 79, 30, 30, 16, 16, 4, 1, 95, 147, 147, 201, 201, 201, 201, 201] 201 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, 34, 35]) total number of confs: 785 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045524 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045524 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045524/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045524 Building REAL250005045525 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045525' /scratch/stefan/7916127/working/building/REAL250005045525 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045525 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045525/0 /scratch/stefan/7916127/working/building/REAL250005045525 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/659 `/scratch/stefan/7916127/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCOC1) `REAL250005045525.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045525 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCOC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 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, 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, 131, 131, 132, 55, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 182, 182, 182, 182, 182, 183, 183, 182, 132, 55, 55, 35, 35, 11, 1, 183, 183, 182, 182, 182, 182, 182, 182] 183 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 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: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045525 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCOC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 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, 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: [1, 1, 1, 5, 5, 5, 29, 56, 170, 171, 170, 182, 183, 183, 182, 182, 1, 1, 1, 1, 1, 2, 2, 2, 5, 29, 29, 56, 56, 171, 182, 1, 1, 1, 1, 1, 1, 1, 1] 183 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 16, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 589 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045525 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045525 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045525/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045525 Building REAL250005045526 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045526' /scratch/stefan/7916127/working/building/REAL250005045526 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045526 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045526/0 /scratch/stefan/7916127/working/building/REAL250005045526 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/660 `/scratch/stefan/7916127/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1) `REAL250005045526.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045526 none CCN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 139, 139, 139, 129, 129, 129, 46, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201, 139, 129, 46, 46, 24, 24, 5, 1] 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]) 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: REAL250005045526 none CCN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 1, 1, 1, 1, 6, 6, 6, 28, 51, 133, 133, 133, 139, 139, 139, 139, 139, 1, 1, 8, 8, 8, 8, 8, 1, 6, 28, 28, 51, 51, 132, 139] 201 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045526 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045526 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045526/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045526 Building REAL250005045527 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045527' /scratch/stefan/7916127/working/building/REAL250005045527 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045527 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045527/0 /scratch/stefan/7916127/working/building/REAL250005045527 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/661 `/scratch/stefan/7916127/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045527.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045527 none CCC1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 170, 170, 170, 170, 121, 121, 121, 43, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 170, 170, 170, 170, 170, 170, 121, 43, 43, 28, 28, 7, 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: 742 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: REAL250005045527 none CCC1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 67, 159, 159, 159, 170, 170, 170, 170, 170, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 7, 41, 41, 67, 67, 159, 170] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 28, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 582 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045527 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045527 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045527/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045527 Building REAL250005045528 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045528' /scratch/stefan/7916127/working/building/REAL250005045528 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045528 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045528/0 /scratch/stefan/7916127/working/building/REAL250005045528 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/662 `/scratch/stefan/7916127/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045528.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045528 none CC(C)C1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 193, 138, 138, 138, 56, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 193, 193, 193, 193, 193, 193, 138, 56, 56, 32, 32, 9, 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: 698 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: REAL250005045528 none CC(C)C1(C)CC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 1, 8, 8, 8, 43, 77, 175, 175, 175, 193, 193, 193, 193, 193, 8, 8, 8, 7, 7, 7, 7, 2, 2, 2, 1, 1, 1, 8, 43, 43, 77, 77, 175, 193] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 664 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045528 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045528 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045528/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045528 Building REAL250005045529 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045529' /scratch/stefan/7916127/working/building/REAL250005045529 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045529 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045529/0 /scratch/stefan/7916127/working/building/REAL250005045529 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/663 `/scratch/stefan/7916127/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045529.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045529 none COCC(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 165, 108, 169, 21, 21, 21, 19, 12, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 197, 201, 170, 170, 170, 170, 108, 108, 21, 19, 19, 12, 12, 3, 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: 905 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045529 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045529 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045529/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045529 Building REAL250005045530 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045530' /scratch/stefan/7916127/working/building/REAL250005045530 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045530 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045530/0 /scratch/stefan/7916127/working/building/REAL250005045530 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/664 `/scratch/stefan/7916127/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045530.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045530 none COCCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 185, 167, 116, 60, 116, 116, 60, 60, 22, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 185, 185, 173, 173, 116, 116, 116, 116, 116, 116, 60, 22, 22, 14, 14, 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: 871 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045530 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045530 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045530/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045530 Building REAL250005045531 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045531' /scratch/stefan/7916127/working/building/REAL250005045531 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045531 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045531/0 /scratch/stefan/7916127/working/building/REAL250005045531 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/665 `/scratch/stefan/7916127/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005045531.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045531 none CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [196, 195, 100, 100, 100, 45, 33, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 195, 195, 195, 195, 196, 196, 196, 196, 196, 100, 45, 45, 33, 33, 11, 1, 195, 195, 195, 195, 195, 195, 195, 195] 196 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: 648 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: REAL250005045531 none CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 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 196 conformations in input total number of sets (complete confs): 196 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 5, 5, 5, 30, 55, 168, 170, 168, 195, 195, 195, 195, 195, 1, 1, 1, 1, 4, 4, 4, 4, 4, 5, 30, 30, 55, 55, 170, 195, 1, 1, 1, 1, 1, 1, 1, 1] 196 rigid atoms, others: [1, 2, 3, 36, 37, 35, 33, 40, 39, 34, 17, 18, 19, 20, 38] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 603 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045531 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045531 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045531/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045531 Building REAL250005045532 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045532' /scratch/stefan/7916127/working/building/REAL250005045532 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045532 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045532/0 /scratch/stefan/7916127/working/building/REAL250005045532 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/666 `/scratch/stefan/7916127/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NON=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045532.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045532 none CC1=NON=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 188, 103, 103, 103, 37, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 188, 188, 103, 37, 37, 24, 24, 4, 1] 201 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: 707 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045532 none CC1=NON=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 30, 76, 106, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 7, 7, 30, 76, 76, 106, 106, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045532 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045532 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045532/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045532 Building REAL250005045533 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045533' /scratch/stefan/7916127/working/building/REAL250005045533 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045533 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045533/0 /scratch/stefan/7916127/working/building/REAL250005045533 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/667 `/scratch/stefan/7916127/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045533.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045533 none O=C(COC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 130, 181, 201, 201, 201, 201, 20, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 130, 130, 201, 201, 201, 201, 201, 201, 201, 63, 20, 20, 11, 11, 3, 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: 688 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045533 none O=C(COC1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 15, 5, 1, 1, 1, 1, 1, 1, 45, 45, 120, 134, 201, 201, 201, 201, 201, 201, 201, 201, 15, 15, 1, 1, 1, 1, 1, 1, 1, 45, 120, 120, 134, 134, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045533 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045533 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045533/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045533 Building REAL250005045534 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045534' /scratch/stefan/7916127/working/building/REAL250005045534 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045534 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045534/0 /scratch/stefan/7916127/working/building/REAL250005045534 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/668 `/scratch/stefan/7916127/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)NC(N)=O) `REAL250005045534.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045534 none CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)NC(N)=O 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', 'N.am', 'C.2', 'N.am', 'O.2', '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, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 4, 6, 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: [121, 85, 48, 48, 48, 19, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 122, 127, 127, 127, 122, 122, 122, 122, 85, 85, 48, 19, 19, 13, 13, 4, 1, 127, 127, 127] 127 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36]) total number of confs: 550 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045534 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045534 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045534/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045534 Building REAL250005045535 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045535' /scratch/stefan/7916127/working/building/REAL250005045535 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045535 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045535/0 /scratch/stefan/7916127/working/building/REAL250005045535 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/669 `/scratch/stefan/7916127/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(C(F)F)CC1)C1=CC(=O)[N-]O1) `REAL250005045535.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045535 none O=C(NCCNC(=O)C1(C(F)F)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 8, 8, 13, 13, 26, 26, 26, 35, 40, 40, 35, 35, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 13, 26, 40, 35, 35, 35, 35, 1] 40 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 135 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: REAL250005045535 none O=C(NCCNC(=O)C1(C(F)F)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 22, 18, 7, 7, 1, 7, 1, 1, 11, 11, 1, 1, 24, 35, 35, 35, 35, 35, 24, 22, 22, 18, 18, 7, 11, 1, 1, 1, 1, 35] 40 rigid atoms, others: [6, 8, 9, 12, 13, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045535 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045535 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045535/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045535 Building REAL250005045536 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045536' /scratch/stefan/7916127/working/building/REAL250005045536 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045536 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045536/0 /scratch/stefan/7916127/working/building/REAL250005045536 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/670 `/scratch/stefan/7916127/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC(F)C1)C1=CC(=O)[N-]O1) `REAL250005045536.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045536 none O=C(NCCNC(=O)C1CCC(F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 35, 48, 121, 121, 121, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 10, 35, 35, 48, 48, 121, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 635 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: REAL250005045536 none O=C(NCCNC(=O)C1CCC(F)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 186, 107, 61, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 186, 201, 201, 201, 201, 201, 187, 107, 107, 61, 61, 11, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 729 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045536 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045536 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045536/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045536 Building REAL250005045537 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045537' /scratch/stefan/7916127/working/building/REAL250005045537 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045537 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045537/0 /scratch/stefan/7916127/working/building/REAL250005045537 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/671 `/scratch/stefan/7916127/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045537.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045537 none C[NH+](C)CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 13, 11, 11, 11, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 11, 10, 10, 10, 10, 5, 1, 13, 13, 13, 13] 14 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, 39, 40]) 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: REAL250005045537 none C[NH+](C)CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 6, 6, 6, 10, 10, 11, 11, 11, 13, 13, 13, 13, 13, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 10, 10, 10, 10, 11, 13, 1, 1, 1, 1] 14 rigid atoms, others: [4, 37, 6, 39, 40, 20, 21, 38, 5] set([0, 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045537 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045537 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045537/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045537 Building REAL250005045538 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045538' /scratch/stefan/7916127/working/building/REAL250005045538 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045538 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045538/0 /scratch/stefan/7916127/working/building/REAL250005045538 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/672 `/scratch/stefan/7916127/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CNC(=O)C=N1)C1=CC(=O)[N-]O1) `REAL250005045538.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045538 none O=C(NCCNC(=O)C1=CNC(=O)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 18, 27, 55, 55, 55, 90, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 7, 18, 18, 27, 27, 55, 90, 90, 90, 1] 90 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045538 none O=C(NCCNC(=O)C1=CNC(=O)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 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: [88, 88, 60, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 88, 90, 90, 90, 90, 90, 88, 60, 60, 46, 46, 11, 1, 1, 1, 90] 90 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045538 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045538 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045538/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045538 Building REAL250005045539 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045539' /scratch/stefan/7916127/working/building/REAL250005045539 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045539 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045539/0 /scratch/stefan/7916127/working/building/REAL250005045539 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/673 `/scratch/stefan/7916127/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(CCC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045539.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045539 none CCCC(CCC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [155, 139, 94, 28, 94, 140, 155, 28, 28, 20, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 155, 155, 155, 151, 155, 147, 147, 94, 147, 147, 155, 151, 155, 155, 155, 28, 20, 20, 13, 13, 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: 1104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045539 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045539 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045539/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045539 Building REAL250005045540 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045540' /scratch/stefan/7916127/working/building/REAL250005045540 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045540 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045540/0 /scratch/stefan/7916127/working/building/REAL250005045540 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/674 `/scratch/stefan/7916127/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CCC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045540.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045540 none CC1(CCC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 138, 130, 55, 55, 55, 28, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 145, 145, 131, 131, 55, 28, 28, 18, 18, 4, 1, 201, 201, 201, 201] 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: 847 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: REAL250005045540 none CC1(CCC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 6, 9, 43, 43, 43, 117, 144, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 6, 6, 9, 9, 43, 118, 118, 145, 145, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 37, 34, 18, 19] set([3, 4, 5, 6, 7, 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: 806 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045540 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045540 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045540/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045540 Building REAL250005045541 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045541' /scratch/stefan/7916127/working/building/REAL250005045541 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045541 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045541/0 /scratch/stefan/7916127/working/building/REAL250005045541 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/675 `/scratch/stefan/7916127/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)ON=C1) `REAL250005045541.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045541 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)ON=C1 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', 'O.3', 'N.2', 'C.2', '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, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 118, 118, 120, 60, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 153, 153, 153, 153, 153, 153, 120, 60, 60, 37, 37, 11, 1, 153] 153 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]) total number of confs: 487 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: REAL250005045541 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)ON=C1 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', 'O.3', 'N.2', 'C.2', '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, 12, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 47, 86, 143, 143, 143, 153, 153, 153, 153, 153, 1, 1, 1, 2, 2, 2, 10, 47, 47, 86, 86, 143, 153, 1] 153 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 579 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045541 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045541 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045541/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045541 Building REAL250005045542 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045542' /scratch/stefan/7916127/working/building/REAL250005045542 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045542 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045542/0 /scratch/stefan/7916127/working/building/REAL250005045542 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/676 `/scratch/stefan/7916127/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(F)CCCCC1)C1=CC(=O)[N-]O1) `REAL250005045542.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045542 none O=C(NCCNC(=O)C1(F)CCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 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: [10, 1, 10, 9, 31, 38, 97, 97, 97, 165, 165, 165, 165, 165, 165, 1, 1, 1, 1, 1, 1, 10, 31, 31, 38, 38, 97, 165, 165, 165, 165, 165, 165, 165, 165, 165, 165, 1] 165 rigid atoms, others: [1, 37, 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]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045542 none O=C(NCCNC(=O)C1(F)CCCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 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: [158, 158, 98, 76, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 158, 165, 165, 165, 165, 165, 158, 98, 98, 76, 76, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 165] 165 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045542 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045542 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045542/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045542 Building REAL250005045543 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045543' /scratch/stefan/7916127/working/building/REAL250005045543 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045543 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045543/0 /scratch/stefan/7916127/working/building/REAL250005045543 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/677 `/scratch/stefan/7916127/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045543.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045543 none CC[N@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 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, 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, 28, 18, 28, 28, 18, 9, 9, 9, 7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 28, 28, 28, 18, 18, 18, 18, 9, 7, 7, 7, 7, 4, 1] 29 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: 137 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045543 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045543/1 /scratch/stefan/7916127/working/building/REAL250005045543 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/678 `/scratch/stefan/7916127/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[N@@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045543.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005045543 none CC[N@@H+](C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 6, 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, 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, 28, 18, 28, 28, 18, 9, 9, 9, 7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 28, 28, 28, 18, 18, 18, 18, 9, 7, 7, 7, 7, 4, 1] 29 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: 137 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045543 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045543 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045543/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045543/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045543 Building REAL250005045544 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045544' /scratch/stefan/7916127/working/building/REAL250005045544 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045544 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045544/0 /scratch/stefan/7916127/working/building/REAL250005045544 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/679 `/scratch/stefan/7916127/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC12CCCC2)C1=CC(=O)[N-]O1) `REAL250005045544.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045544 none O=C(NCCNC(=O)C1CC12CCCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 28, 48, 123, 123, 123, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 28, 28, 48, 48, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045544 none O=C(NCCNC(=O)C1CC12CCCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [195, 194, 95, 61, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 194, 201, 201, 201, 201, 201, 195, 95, 95, 61, 61, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 712 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045544 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045544 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045544/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045544 Building REAL250005045545 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045545' /scratch/stefan/7916127/working/building/REAL250005045545 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045545 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045545/0 /scratch/stefan/7916127/working/building/REAL250005045545 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/680 `/scratch/stefan/7916127/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CON=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045545.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045545 none CC1=CON=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 82, 82, 39, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 39, 39, 26, 26, 9, 1] 82 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045545 none CC1=CON=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 35, 78, 78, 78, 82, 82, 82, 82, 82, 2, 2, 2, 1, 5, 23, 23, 35, 35, 78, 82] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045545 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045545 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045545/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045545 Building REAL250005045546 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045546' /scratch/stefan/7916127/working/building/REAL250005045546 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045546 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045546/0 /scratch/stefan/7916127/working/building/REAL250005045546 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/681 `/scratch/stefan/7916127/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045546.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045546 none CCOC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 17, 8, 1, 8, 19, 19, 19, 81, 105, 189, 191, 189, 194, 194, 194, 194, 194, 1, 1, 1, 19, 19, 19, 19, 19, 8, 19, 81, 81, 105, 105, 191, 194, 1, 1, 1, 1, 1] 201 rigid atoms, others: [3, 34, 35, 36, 37, 38, 18, 19, 20] set([0, 1, 2, 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, 32, 33]) total number of confs: 734 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: REAL250005045546 none CCOC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 143, 125, 72, 72, 72, 30, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 194, 194, 150, 150, 150, 150, 150, 125, 72, 30, 30, 19, 19, 4, 1, 194, 194, 194, 194, 194] 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, 38]) total number of confs: 836 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045546 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045546 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045546/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045546 Building REAL250005045547 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045547' /scratch/stefan/7916127/working/building/REAL250005045547 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045547 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045547/0 /scratch/stefan/7916127/working/building/REAL250005045547 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/682 `/scratch/stefan/7916127/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CN=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045547.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045547 none O=C(CN1N=CN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 123, 201, 201, 201, 201, 28, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 123, 123, 201, 76, 28, 28, 14, 14, 4, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045547 none O=C(CN1N=CN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 33, 33, 92, 122, 201, 200, 201, 201, 201, 201, 201, 201, 9, 9, 1, 33, 92, 92, 122, 122, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045547 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045547 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045547/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045547 Building REAL250005045548 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045548' /scratch/stefan/7916127/working/building/REAL250005045548 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045548 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045548/0 /scratch/stefan/7916127/working/building/REAL250005045548 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/683 `/scratch/stefan/7916127/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045548.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045548 none CCCC[C@@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 181, 174, 126, 44, 126, 126, 44, 44, 24, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 177, 177, 126, 126, 126, 44, 24, 24, 15, 15, 4, 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: 975 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045548 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045548 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045548/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045548 Building REAL250005045549 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045549' /scratch/stefan/7916127/working/building/REAL250005045549 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045549 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045549/0 /scratch/stefan/7916127/working/building/REAL250005045549 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/684 `/scratch/stefan/7916127/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(CC=C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045549.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045549 none C=CCC(CC=C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 147, 89, 35, 89, 144, 176, 35, 35, 17, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 175, 175, 175, 147, 147, 89, 144, 144, 176, 176, 176, 35, 17, 17, 10, 10, 2, 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: 1213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045549 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045549 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045549/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045549 Building REAL250005045550 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045550' /scratch/stefan/7916127/working/building/REAL250005045550 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045550 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045550/0 /scratch/stefan/7916127/working/building/REAL250005045550 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/685 `/scratch/stefan/7916127/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC=CCC1) `REAL250005045550.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045550 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC=CCC1 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.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [117, 96, 96, 96, 39, 27, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117, 96, 39, 39, 27, 27, 10, 1, 117, 117, 117, 117, 117, 117, 117, 117] 117 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 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: 384 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: REAL250005045550 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC=CCC1 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.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 4, 4, 21, 38, 107, 107, 107, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 2, 2, 2, 4, 21, 21, 38, 38, 107, 117, 1, 1, 1, 1, 1, 1, 1, 1] 117 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 16, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 381 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045550 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045550 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045550/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045550 Building REAL250005045551 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045551' /scratch/stefan/7916127/working/building/REAL250005045551 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045551 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045551/0 /scratch/stefan/7916127/working/building/REAL250005045551 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/686 `/scratch/stefan/7916127/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045551.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045551 none CCC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 146, 73, 146, 146, 29, 29, 29, 21, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 146, 146, 146, 146, 146, 146, 73, 73, 29, 21, 21, 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: 983 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045551 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045551 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045551/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045551 Building REAL250005045552 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045552' /scratch/stefan/7916127/working/building/REAL250005045552 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045552 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045552/0 /scratch/stefan/7916127/working/building/REAL250005045552 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/687 `/scratch/stefan/7916127/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045552.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045552 none CC(C)C(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [166, 152, 166, 77, 153, 153, 77, 77, 37, 24, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 189, 153, 153, 153, 153, 153, 153, 77, 37, 37, 24, 24, 4, 1] 189 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: 1089 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045552 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045552 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045552/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045552 Building REAL250005045553 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045553' /scratch/stefan/7916127/working/building/REAL250005045553 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045553 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045553/0 /scratch/stefan/7916127/working/building/REAL250005045553 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/688 `/scratch/stefan/7916127/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045553.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045553 none C=CC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 103, 199, 199, 37, 37, 37, 23, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103, 37, 23, 23, 16, 16, 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: 882 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045553 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045553 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045553/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045553 Building REAL250005045554 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045554' /scratch/stefan/7916127/working/building/REAL250005045554 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045554 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045554/0 /scratch/stefan/7916127/working/building/REAL250005045554 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/689 `/scratch/stefan/7916127/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1N=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045554.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045554 none O=C(CN1N=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 183, 201, 201, 201, 201, 35, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 183, 183, 201, 201, 70, 35, 35, 22, 22, 4, 1] 201 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]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045554 none O=C(CN1N=CC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 22, 22, 79, 113, 170, 171, 171, 171, 171, 171, 171, 171, 5, 5, 1, 1, 22, 79, 79, 113, 113, 171, 171] 171 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 672 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045554 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045554 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045554/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045554 Building REAL250005045555 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045555' /scratch/stefan/7916127/working/building/REAL250005045555 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045555 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045555/0 /scratch/stefan/7916127/working/building/REAL250005045555 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/690 `/scratch/stefan/7916127/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045555.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045555 none CC1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [154, 154, 154, 154, 154, 154, 123, 123, 123, 52, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 154, 123, 52, 52, 34, 34, 10, 1] 154 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: 515 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045555 none CC1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 41, 72, 143, 143, 143, 154, 154, 154, 154, 154, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 41, 41, 72, 72, 143, 154] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 24, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 545 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045555 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045555 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045555/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045555 Building REAL250005045556 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045556' /scratch/stefan/7916127/working/building/REAL250005045556 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045556 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045556/0 /scratch/stefan/7916127/working/building/REAL250005045556 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/691 `/scratch/stefan/7916127/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045556.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045556 none CC1CCCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 107, 107, 107, 43, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 107, 43, 43, 28, 28, 7, 1, 201, 201] 201 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: 644 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045556 none CC1CCCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 73, 114, 198, 198, 198, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 73, 73, 114, 114, 198, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045556 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045556 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045556/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045556 Building REAL250005045557 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045557' /scratch/stefan/7916127/working/building/REAL250005045557 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045557 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045557/0 /scratch/stefan/7916127/working/building/REAL250005045557 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/692 `/scratch/stefan/7916127/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045557.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045557 none CC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 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: [193, 193, 193, 193, 193, 193, 123, 123, 123, 53, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 193, 193, 193, 193, 193, 193, 123, 53, 53, 36, 36, 10, 1] 193 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]) total number of confs: 521 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045557 none CC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 193 conformations in input total number of sets (complete confs): 193 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 65, 114, 186, 187, 186, 193, 193, 193, 193, 193, 2, 2, 2, 1, 1, 1, 10, 65, 65, 114, 114, 187, 193] 193 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045557 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045557 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045557/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045557 Building REAL250005045558 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045558' /scratch/stefan/7916127/working/building/REAL250005045558 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045558 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045558/0 /scratch/stefan/7916127/working/building/REAL250005045558 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/693 `/scratch/stefan/7916127/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045558.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045558 none C=CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 133, 118, 41, 41, 41, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 192, 192, 153, 153, 118, 118, 41, 27, 27, 16, 16, 4, 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: 992 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045558 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045558 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045558/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045558 Building REAL250005045559 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045559' /scratch/stefan/7916127/working/building/REAL250005045559 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045559 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045559/0 /scratch/stefan/7916127/working/building/REAL250005045559 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/694 `/scratch/stefan/7916127/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045559.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045559 none CCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 164, 69, 163, 163, 69, 69, 35, 24, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 164, 163, 164, 164, 164, 163, 69, 35, 35, 24, 24, 5, 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: 1150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045559 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045559 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045559/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045559 Building REAL250005045560 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045560' /scratch/stefan/7916127/working/building/REAL250005045560 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045560 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045560/0 /scratch/stefan/7916127/working/building/REAL250005045560 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/695 `/scratch/stefan/7916127/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045560.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045560 none CCCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 157, 89, 156, 156, 89, 89, 26, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 157, 156, 157, 157, 157, 156, 89, 26, 26, 16, 16, 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: 942 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045560 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045560 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045560/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045560 Building REAL250005045561 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045561' /scratch/stefan/7916127/working/building/REAL250005045561 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045561 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045561/0 /scratch/stefan/7916127/working/building/REAL250005045561 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/696 `/scratch/stefan/7916127/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045561.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045561 none NC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 6, 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] 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, 99, 127, 56, 56, 56, 20, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 99, 99, 127, 127, 56, 20, 20, 18, 18, 8, 1, 99, 99, 99, 99] 127 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]) total number of confs: 401 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: REAL250005045561 none NC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 6, 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] 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: [7, 1, 7, 1, 1, 7, 7, 7, 38, 60, 83, 83, 83, 99, 99, 99, 99, 99, 1, 1, 7, 7, 7, 38, 38, 60, 60, 83, 99, 1, 1, 1, 1] 127 rigid atoms, others: [32, 1, 3, 4, 18, 19, 29, 30, 31] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 385 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045561 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045561 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045561/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045561 Building REAL250005045562 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045562' /scratch/stefan/7916127/working/building/REAL250005045562 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045562 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045562/0 /scratch/stefan/7916127/working/building/REAL250005045562 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/697 `/scratch/stefan/7916127/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045562.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045562 none CC1=NOC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 99, 99, 99, 45, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 99, 45, 45, 30, 30, 9, 1] 139 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]) total number of confs: 386 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045562 none CC1=NOC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 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 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 53, 83, 135, 135, 135, 139, 139, 139, 139, 139, 2, 2, 2, 1, 12, 53, 53, 83, 83, 135, 139] 139 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 527 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045562 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045562 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045562/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045562 Building REAL250005045563 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045563' /scratch/stefan/7916127/working/building/REAL250005045563 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045563 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045563/0 /scratch/stefan/7916127/working/building/REAL250005045563 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/698 `/scratch/stefan/7916127/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCCC1) `REAL250005045563.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045563 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCCC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 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, 122, 122, 122, 53, 38, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 172, 174, 174, 174, 172, 174, 174, 174, 122, 53, 53, 38, 38, 11, 1, 172, 174, 174, 174, 174, 174, 174, 174, 174, 172] 174 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 610 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045563 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCCC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 2, 2, 2, 18, 41, 147, 148, 147, 174, 174, 174, 174, 174, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 41, 41, 148, 174, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 174 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 40, 39, 34, 16, 17, 18, 19, 20, 21, 22, 23, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 505 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045563 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045563 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045563/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045563 Building REAL250005045564 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045564' /scratch/stefan/7916127/working/building/REAL250005045564 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045564 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045564/0 /scratch/stefan/7916127/working/building/REAL250005045564 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/699 `/scratch/stefan/7916127/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045564.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045564 none C[NH+]1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 65, 65, 65, 29, 27, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 65, 29, 29, 27, 27, 11, 1, 99, 99, 99, 99] 99 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, 39, 40]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045564 none C[NH+]1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 46, 61, 71, 71, 71, 99, 99, 99, 99, 99, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 13, 46, 46, 61, 61, 71, 99, 1, 1, 1, 1] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 40, 20, 21, 25, 26, 27, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045564 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045564 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045564/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045564 Building REAL250005045565 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045565' /scratch/stefan/7916127/working/building/REAL250005045565 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045565 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045565/0 /scratch/stefan/7916127/working/building/REAL250005045565 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/700 `/scratch/stefan/7916127/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC=CC1) `REAL250005045565.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045565 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC=CC1 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.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 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, 4, 7, 6, 7, 7, 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, 111, 111, 111, 46, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 111, 46, 46, 29, 29, 7, 1, 201, 201, 201, 201, 201, 201] 201 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: 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: REAL250005045565 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC=CC1 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.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 1, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 5, 35, 68, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 5, 35, 35, 68, 68, 193, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 680 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045565 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045565 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045565/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045565 Building REAL250005045566 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045566' /scratch/stefan/7916127/working/building/REAL250005045566 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045566 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045566/0 /scratch/stefan/7916127/working/building/REAL250005045566 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/701 `/scratch/stefan/7916127/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC1=O) `REAL250005045566.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045566 none CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 86, 86, 86, 36, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 86, 36, 36, 26, 26, 9, 1, 130] 130 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]) total number of confs: 355 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045566 none CN1C=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 49, 69, 121, 121, 121, 130, 130, 130, 130, 130, 1, 1, 1, 2, 2, 2, 1, 13, 49, 49, 69, 69, 121, 130, 1] 130 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 469 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045566 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045566 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045566/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045566 Building REAL250005045567 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045567' /scratch/stefan/7916127/working/building/REAL250005045567 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045567 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045567/0 /scratch/stefan/7916127/working/building/REAL250005045567 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/702 `/scratch/stefan/7916127/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005045567.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045567 none COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C 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', '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, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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: [170, 157, 110, 110, 110, 43, 24, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 157, 199, 199, 170, 170, 170, 157, 110, 43, 43, 24, 24, 4, 1, 199, 199, 199, 199, 199, 199, 199] 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, 35, 36, 37]) total number of confs: 883 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045567 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045567 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045567/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045567 Building REAL250005045568 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045568' /scratch/stefan/7916127/working/building/REAL250005045568 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045568 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045568/0 /scratch/stefan/7916127/working/building/REAL250005045568 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/703 `/scratch/stefan/7916127/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045568.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045568 none CC1CC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 61, 61, 61, 31, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 162, 162, 61, 31, 31, 21, 21, 4, 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: 773 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045568 none CC1CC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 6, 37, 37, 37, 106, 124, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 6, 6, 37, 106, 106, 124, 124, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 22, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045568 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045568 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045568/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045568 Building REAL250005045569 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045569' /scratch/stefan/7916127/working/building/REAL250005045569 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045569 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045569/0 /scratch/stefan/7916127/working/building/REAL250005045569 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/704 `/scratch/stefan/7916127/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045569.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045569 none CCCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need 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, 178, 147, 53, 53, 53, 21, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 147, 147, 201, 201, 201, 201, 201, 197, 197, 178, 178, 53, 21, 21, 13, 13, 4, 1, 147, 147, 147, 147] 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: 749 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: REAL250005045569 none CCCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [10, 7, 5, 1, 1, 1, 7, 7, 7, 42, 59, 142, 146, 146, 147, 147, 147, 147, 147, 1, 1, 10, 11, 11, 11, 11, 7, 7, 5, 5, 7, 42, 42, 59, 59, 146, 147, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 38, 39, 40, 19, 20, 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, 35, 36]) total number of confs: 558 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045569 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045569 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045569/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045569 Building REAL250005045570 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045570' /scratch/stefan/7916127/working/building/REAL250005045570 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045570 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045570/0 /scratch/stefan/7916127/working/building/REAL250005045570 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/705 `/scratch/stefan/7916127/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045570.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045570 none C=C1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 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, 117, 117, 117, 48, 32, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 48, 48, 32, 32, 7, 1, 201, 201, 201, 201] 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: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045570 none C=C1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 13, 13, 13, 66, 110, 191, 191, 191, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 66, 66, 110, 110, 191, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 38, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 36] set([32, 33, 34, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31]) total number of confs: 710 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045570 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045570 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045570/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045570 Building REAL250005045571 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045571' /scratch/stefan/7916127/working/building/REAL250005045571 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045571 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045571/0 /scratch/stefan/7916127/working/building/REAL250005045571 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/706 `/scratch/stefan/7916127/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045571.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045571 none C=CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 162, 129, 49, 49, 49, 22, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 129, 129, 201, 201, 201, 201, 201, 162, 162, 49, 22, 22, 14, 14, 4, 1, 129, 129, 129, 129] 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: 820 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: REAL250005045571 none C=CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 5, 1, 1, 1, 6, 6, 6, 40, 53, 122, 122, 122, 129, 129, 129, 129, 129, 1, 1, 19, 19, 19, 8, 8, 5, 5, 6, 40, 40, 53, 53, 122, 129, 1, 1, 1, 1] 201 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: 489 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045571 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045571 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045571/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045571 Building REAL250005045572 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045572' /scratch/stefan/7916127/working/building/REAL250005045572 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045572 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045572/0 /scratch/stefan/7916127/working/building/REAL250005045572 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/707 `/scratch/stefan/7916127/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045572.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045572 none C=CC(C)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 169, 84, 167, 169, 183, 84, 84, 33, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 188, 188, 188, 169, 169, 167, 201, 201, 201, 201, 201, 84, 33, 33, 20, 20, 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: 1059 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045572 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045572 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045572/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045572 Building REAL250005045573 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045573' /scratch/stefan/7916127/working/building/REAL250005045573 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045573 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045573/0 /scratch/stefan/7916127/working/building/REAL250005045573 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/708 `/scratch/stefan/7916127/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC(F)CC1)C1=CC(=O)[N-]O1) `REAL250005045573.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045573 none O=C(NCCNC(=O)C1CCC(F)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 29, 46, 123, 123, 123, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 29, 29, 46, 46, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 37, 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]) total number of confs: 654 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045573 none O=C(NCCNC(=O)C1CCC(F)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens 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, 195, 114, 75, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 195, 201, 201, 201, 201, 201, 197, 114, 114, 75, 75, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 750 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045573 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045573 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045573/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045573 Building REAL250005045574 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045574' /scratch/stefan/7916127/working/building/REAL250005045574 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045574 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045574/0 /scratch/stefan/7916127/working/building/REAL250005045574 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/709 `/scratch/stefan/7916127/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045574.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045574 none O=C(C[C@H]1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 148, 201, 201, 201, 201, 201, 33, 20, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 149, 149, 201, 201, 201, 201, 201, 201, 57, 33, 33, 19, 19, 4, 1] 201 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: 817 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045574 none O=C(C[C@H]1CCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 7, 5, 5, 12, 5, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 6, 1, 1, 1, 1, 1, 1, 1, 35, 35, 109, 136, 201, 201, 201, 201, 201, 201, 201, 201, 6, 6, 1, 1, 1, 1, 1, 1, 35, 109, 109, 136, 136, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045574 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045574 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045574/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045574 Building REAL250005045575 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045575' /scratch/stefan/7916127/working/building/REAL250005045575 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045575 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045575/0 /scratch/stefan/7916127/working/building/REAL250005045575 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/710 `/scratch/stefan/7916127/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045575.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045575 none C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 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, 64, 64, 64, 28, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 164, 164, 164, 201, 201, 201, 201, 201, 64, 28, 28, 17, 17, 4, 1, 164, 164, 164, 164, 164, 164] 201 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: 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: REAL250005045575 none C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 7, 7, 7, 44, 62, 148, 152, 152, 164, 164, 164, 164, 164, 1, 1, 1, 22, 22, 22, 5, 5, 7, 44, 44, 62, 62, 152, 164, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 2, 3, 4, 37, 35, 34, 18, 19, 20, 36, 38] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045575 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045575 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045575/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045575 Building REAL250005045576 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045576' /scratch/stefan/7916127/working/building/REAL250005045576 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045576 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045576/0 /scratch/stefan/7916127/working/building/REAL250005045576 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/711 `/scratch/stefan/7916127/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045576.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045576 none O=C(CC1=CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 1, 1, 5, 12, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 164, 201, 201, 201, 201, 201, 35, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 164, 164, 201, 201, 201, 201, 201, 201, 201, 62, 35, 35, 23, 23, 6, 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: 701 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045576 none O=C(CC1=CCOCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 1, 1, 5, 12, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 1, 43, 43, 114, 120, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1, 43, 114, 114, 120, 120, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045576 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045576 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045576/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045576 Building REAL250005045577 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045577' /scratch/stefan/7916127/working/building/REAL250005045577 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045577 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045577/0 /scratch/stefan/7916127/working/building/REAL250005045577 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/712 `/scratch/stefan/7916127/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=C1) `REAL250005045577.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045577 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 155, 155, 122, 122, 122, 41, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 155, 155, 155, 201, 201, 201, 201, 201, 122, 41, 41, 25, 25, 4, 1, 155, 155] 201 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: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045577 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 1, 1, 1, 7, 7, 7, 39, 62, 147, 147, 147, 154, 154, 154, 154, 154, 1, 1, 1, 6, 6, 6, 6, 6, 7, 39, 39, 62, 62, 147, 154, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 34, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045577 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045577 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045577/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045577 Building REAL250005045578 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045578' /scratch/stefan/7916127/working/building/REAL250005045578 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045578 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045578/0 /scratch/stefan/7916127/working/building/REAL250005045578 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/713 `/scratch/stefan/7916127/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045578.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045578 none CCC1(C(=O)NCCNC(=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', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 78, 78, 78, 35, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 180, 180, 201, 201, 201, 201, 201, 78, 35, 35, 25, 25, 4, 1, 180, 180, 180, 180] 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: 682 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: REAL250005045578 none CCC1(C(=O)NCCNC(=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', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 7, 7, 7, 45, 77, 180, 180, 180, 180, 180, 180, 180, 180, 1, 1, 4, 4, 4, 4, 4, 7, 45, 45, 77, 77, 180, 180, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 33, 34, 17, 18, 31] set([0, 4, 5, 6, 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: 643 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045578 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045578 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045578/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045578 Building REAL250005045579 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045579' /scratch/stefan/7916127/working/building/REAL250005045579 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045579 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045579/0 /scratch/stefan/7916127/working/building/REAL250005045579 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/714 `/scratch/stefan/7916127/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005045579.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045579 none CC(C)[C@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 11, 12, 11, 11, 11, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 10, 10, 3, 1, 12, 12, 12, 12, 12, 12] 12 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, 41, 42]) total number of confs: 43 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045579 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045579 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045579/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045579 Building REAL250005045580 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045580' /scratch/stefan/7916127/working/building/REAL250005045580 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045580 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045580/0 /scratch/stefan/7916127/working/building/REAL250005045580 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/715 `/scratch/stefan/7916127/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045580.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045580 none CCC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 92, 92, 81, 80, 81, 43, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 81, 43, 43, 30, 30, 11, 1] 92 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: 320 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: REAL250005045580 none CCC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 28, 81, 81, 81, 92, 92, 92, 92, 92, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 16, 16, 28, 28, 81, 92] 92 rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 33, 26, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 292 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045580 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045580 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045580/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045580 Building REAL250005045581 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045581' /scratch/stefan/7916127/working/building/REAL250005045581 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045581 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045581/0 /scratch/stefan/7916127/working/building/REAL250005045581 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/716 `/scratch/stefan/7916127/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045581.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045581 none CC(C)(C)C(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 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, 70, 74, 74, 70, 70, 41, 27, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74, 70, 41, 41, 27, 27, 8, 1] 74 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: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045581 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045581 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045581/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045581 Building REAL250005045582 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045582' /scratch/stefan/7916127/working/building/REAL250005045582 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045582 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045582/0 /scratch/stefan/7916127/working/building/REAL250005045582 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/717 `/scratch/stefan/7916127/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1) `REAL250005045582.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045582 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 49, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 49, 49, 36, 36, 11, 1, 77, 77] 77 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]) total number of confs: 286 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045582 none CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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, 3, 3, 3, 15, 35, 67, 67, 67, 77, 77, 77, 77, 77, 1, 1, 2, 2, 2, 1, 1, 3, 15, 15, 35, 35, 67, 77, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 19, 20, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045582 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045582 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045582/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045582 Building REAL250005045583 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045583' /scratch/stefan/7916127/working/building/REAL250005045583 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045583 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045583/0 /scratch/stefan/7916127/working/building/REAL250005045583 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/718 `/scratch/stefan/7916127/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC12CCOC2)C1=CC(=O)[N-]O1) `REAL250005045583.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045583 none O=C(NCCNC(=O)C1CC12CCOC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 34, 57, 129, 130, 129, 194, 194, 194, 194, 194, 194, 1, 1, 1, 1, 1, 1, 8, 34, 34, 57, 57, 130, 194, 194, 194, 194, 194, 194, 194, 194, 194, 1] 194 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: 667 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: REAL250005045583 none O=C(NCCNC(=O)C1CC12CCOC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 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 194 conformations in input total number of sets (complete confs): 194 using faster count positions algorithm for large data unique positions, atoms: [183, 182, 82, 52, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 182, 194, 194, 194, 194, 194, 183, 82, 82, 52, 52, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 194] 194 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 653 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045583 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045583 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045583/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045583 Building REAL250005045584 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045584' /scratch/stefan/7916127/working/building/REAL250005045584 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045584 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045584/0 /scratch/stefan/7916127/working/building/REAL250005045584 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/719 `/scratch/stefan/7916127/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045584.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045584 none COCCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 141, 141, 99, 42, 99, 42, 42, 15, 10, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 141, 141, 141, 99, 99, 99, 99, 42, 15, 15, 10, 10, 3, 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: 929 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045584 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045584 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045584/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045584 Building REAL250005045585 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045585' /scratch/stefan/7916127/working/building/REAL250005045585 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045585 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045585/0 /scratch/stefan/7916127/working/building/REAL250005045585 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/720 `/scratch/stefan/7916127/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC(C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045585.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045585 none CCC(CC(C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [159, 146, 71, 146, 151, 151, 151, 71, 71, 33, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 146, 151, 151, 151, 151, 151, 151, 151, 151, 151, 71, 33, 33, 21, 21, 4, 1] 170 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: 813 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045585 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045585 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045585/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045585 Building REAL250005045586 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045586' /scratch/stefan/7916127/working/building/REAL250005045586 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045586 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045586/0 /scratch/stefan/7916127/working/building/REAL250005045586 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/721 `/scratch/stefan/7916127/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045586.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045586 none CC(C)CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 73, 80, 80, 73, 73, 29, 18, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 73, 29, 29, 18, 18, 9, 1] 80 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: 271 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045586 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045586 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045586/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045586 Building REAL250005045587 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045587' /scratch/stefan/7916127/working/building/REAL250005045587 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045587 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045587/0 /scratch/stefan/7916127/working/building/REAL250005045587 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/722 `/scratch/stefan/7916127/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045587.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045587 none NC(=O)CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 153, 201, 93, 90, 91, 31, 31, 31, 23, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 153, 153, 93, 93, 93, 93, 91, 91, 31, 23, 23, 18, 18, 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: 885 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045587 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045587 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045587/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045587 Building REAL250005045588 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045588' /scratch/stefan/7916127/working/building/REAL250005045588 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045588 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045588/0 /scratch/stefan/7916127/working/building/REAL250005045588 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/723 `/scratch/stefan/7916127/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C(C1CC1)C1CC1)C1=CC(=O)[N-]O1) `REAL250005045588.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045588 none O=C(NCCNC(=O)C(C1CC1)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [200, 197, 117, 81, 22, 22, 5, 22, 1, 5, 8, 8, 1, 1, 1, 197, 201, 201, 201, 201, 201, 200, 117, 117, 81, 81, 22, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 8, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38]) total number of confs: 790 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045588 none O=C(NCCNC(=O)C(C1CC1)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [5, 1, 5, 5, 24, 39, 94, 94, 94, 198, 200, 200, 200, 201, 201, 1, 1, 1, 1, 1, 1, 5, 24, 24, 39, 39, 94, 200, 200, 200, 200, 200, 200, 201, 201, 201, 201, 201, 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: 775 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045588 none O=C(NCCNC(=O)C(C1CC1)C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [200, 198, 117, 82, 20, 20, 4, 20, 1, 1, 1, 1, 4, 8, 8, 198, 200, 200, 200, 200, 200, 200, 117, 117, 82, 82, 20, 4, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 200] 201 rigid atoms, others: [32, 8, 9, 10, 11, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045588 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045588 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045588/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045588 Building REAL250005045589 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045589' /scratch/stefan/7916127/working/building/REAL250005045589 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045589 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045589/0 /scratch/stefan/7916127/working/building/REAL250005045589 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/724 `/scratch/stefan/7916127/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045589.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045589 none O=C(CC1=NNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 101, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 101, 101, 201, 201, 54, 23, 23, 14, 14, 4, 1] 201 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]) total number of confs: 560 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045589 none O=C(CC1=NNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 9, 1, 1, 1, 1, 1, 1, 41, 41, 117, 140, 201, 201, 201, 201, 201, 201, 201, 200, 9, 9, 1, 1, 41, 117, 117, 140, 140, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045589 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045589/1 /scratch/stefan/7916127/working/building/REAL250005045589 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/725 `/scratch/stefan/7916127/working/3D/725' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045589.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045589 none O=C(CC1=NN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 4, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 83, 83, 83, 83, 83, 17, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 41, 17, 17, 10, 10, 4, 1] 83 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]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045589 none O=C(CC1=NN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 4, 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 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [13, 5, 1, 1, 1, 1, 1, 1, 13, 13, 33, 43, 83, 83, 83, 83, 83, 83, 83, 83, 5, 5, 1, 1, 13, 33, 33, 43, 43, 83, 83] 83 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 320 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045589 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045589 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045589/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045589/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045589 Building REAL250005045590 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045590' /scratch/stefan/7916127/working/building/REAL250005045590 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045590 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045590/0 /scratch/stefan/7916127/working/building/REAL250005045590 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/726 `/scratch/stefan/7916127/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCCC1) `REAL250005045590.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045590 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCCC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 16, 16, 16, 70, 98, 192, 192, 192, 192, 192, 192, 192, 192, 1, 1, 1, 1, 1, 3, 3, 3, 2, 16, 70, 70, 98, 98, 192, 192, 1, 1, 1, 1, 1, 1, 1, 1, 1] 192 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 40, 39, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005045590 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCCC1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 104, 104, 104, 41, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192, 104, 41, 41, 26, 26, 4, 1, 192, 192, 192, 192, 192, 192, 192, 192, 192] 192 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045590 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045590 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045590/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045590 Building REAL250005045591 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045591' /scratch/stefan/7916127/working/building/REAL250005045591 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045591 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045591/0 /scratch/stefan/7916127/working/building/REAL250005045591 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/727 `/scratch/stefan/7916127/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005045591.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045591 none CCCC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', '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', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 173, 126, 45, 45, 45, 27, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 126, 179, 168, 196, 196, 196, 196, 194, 175, 175, 126, 45, 27, 27, 17, 17, 4, 1, 179, 179, 179, 179, 179, 179, 179] 201 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, 39, 40, 41, 42]) total number of confs: 1260 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045591 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045591 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045591/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045591 Building REAL250005045592 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045592' /scratch/stefan/7916127/working/building/REAL250005045592 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045592 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045592/0 /scratch/stefan/7916127/working/building/REAL250005045592 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/728 `/scratch/stefan/7916127/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1C=CC=CC=C1)C1=CC(=O)[N-]O1) `REAL250005045592.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045592 none O=C(NCCNC(=O)C1C=CC=CC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 0 hydrogens need rotated 117 conformations in input total number of sets (complete confs): 117 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 30, 41, 95, 95, 95, 117, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 9, 30, 30, 41, 41, 95, 117, 117, 117, 117, 117, 117, 117, 1] 117 rigid atoms, others: [1, 34, 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]) total number of confs: 394 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045592 none O=C(NCCNC(=O)C1C=CC=CC=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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] 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: [111, 111, 39, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 111, 117, 117, 117, 117, 117, 111, 39, 39, 24, 24, 4, 1, 1, 1, 1, 1, 1, 1, 117] 117 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045592 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045592 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045592/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045592 Building REAL250005045593 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045593' /scratch/stefan/7916127/working/building/REAL250005045593 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045593 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045593/0 /scratch/stefan/7916127/working/building/REAL250005045593 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/729 `/scratch/stefan/7916127/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045593.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045593 none C=C(C)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 199, 184, 86, 86, 86, 44, 26, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 200, 200, 201, 201, 201, 201, 185, 185, 86, 44, 44, 26, 26, 6, 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: 867 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045593 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045593 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045593/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045593 Building REAL250005045594 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045594' /scratch/stefan/7916127/working/building/REAL250005045594 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045594 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045594/0 /scratch/stefan/7916127/working/building/REAL250005045594 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/730 `/scratch/stefan/7916127/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=NS1)C1=CC(=O)[N-]O1) `REAL250005045594.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045594 none O=C(NCCNC(=O)C1=CC=NS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [7, 1, 7, 7, 24, 39, 77, 77, 77, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 7, 24, 24, 39, 39, 77, 109, 109, 1] 109 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 332 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045594 none O=C(NCCNC(=O)C1=CC=NS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 8, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [105, 105, 67, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 105, 109, 109, 109, 109, 109, 105, 67, 67, 42, 42, 13, 1, 1, 109] 109 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045594 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045594 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045594/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045594 Building REAL250005045595 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045595' /scratch/stefan/7916127/working/building/REAL250005045595 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045595 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045595/0 /scratch/stefan/7916127/working/building/REAL250005045595 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/731 `/scratch/stefan/7916127/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045595.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045595 none CCC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 192, 192, 192, 105, 105, 105, 37, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 192, 201, 201, 201, 201, 201, 192, 192, 192, 192, 192, 192, 105, 37, 37, 21, 21, 4, 1] 201 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]) total number of confs: 659 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: REAL250005045595 none CCC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 83, 183, 183, 183, 192, 192, 192, 192, 192, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 11, 56, 56, 83, 83, 183, 192] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26, 27, 28, 29, 30, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 665 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045595 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045595 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045595/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045595 Building REAL250005045596 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045596' /scratch/stefan/7916127/working/building/REAL250005045596 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045596 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045596/0 /scratch/stefan/7916127/working/building/REAL250005045596 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/732 `/scratch/stefan/7916127/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045596.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045596 none COCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 126, 102, 43, 43, 43, 19, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 102, 102, 201, 201, 201, 198, 198, 126, 126, 43, 19, 19, 13, 13, 4, 1, 102, 102, 102, 102] 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: 861 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045596 none COCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 6, 6, 6, 36, 55, 92, 92, 92, 102, 102, 102, 102, 102, 1, 1, 27, 27, 27, 10, 10, 6, 6, 6, 36, 36, 55, 55, 92, 102, 1, 1, 1, 1] 201 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: 429 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045596 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045596 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045596/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045596 Building REAL250005045597 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045597' /scratch/stefan/7916127/working/building/REAL250005045597 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045597 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045597/0 /scratch/stefan/7916127/working/building/REAL250005045597 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/733 `/scratch/stefan/7916127/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045597.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045597 none CC(C)CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 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, 115, 115, 115, 39, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 39, 39, 25, 25, 5, 1, 201, 201, 201, 201] 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: 643 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: REAL250005045597 none CC(C)CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 1, 1, 1, 6, 6, 6, 38, 73, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 38, 38, 73, 73, 197, 201, 1, 1, 1, 1] 201 rigid atoms, others: [3, 4, 5, 38, 39, 40, 19, 20, 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, 35, 36]) total number of confs: 678 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045597 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045597 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045597/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045597 Building REAL250005045598 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045598' /scratch/stefan/7916127/working/building/REAL250005045598 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045598 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045598/0 /scratch/stefan/7916127/working/building/REAL250005045598 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/734 `/scratch/stefan/7916127/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045598.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045598 none COCC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 87, 66, 86, 29, 66, 29, 29, 20, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 87, 87, 87, 87, 66, 66, 66, 66, 29, 20, 20, 13, 13, 4, 1] 115 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: 540 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045598 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045598 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045598/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045598 Building REAL250005045599 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045599' /scratch/stefan/7916127/working/building/REAL250005045599 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045599 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045599/0 /scratch/stefan/7916127/working/building/REAL250005045599 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/735 `/scratch/stefan/7916127/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCNC1=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045599.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045599 none O=C(CC1CCNC1=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 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] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 102, 107, 107, 107, 107, 107, 34, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 102, 102, 107, 107, 107, 107, 107, 107, 67, 34, 34, 22, 22, 4, 1] 107 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: 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: REAL250005045599 none O=C(CC1CCNC1=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 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] 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: [19, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19, 50, 62, 107, 107, 107, 107, 107, 107, 107, 107, 7, 7, 1, 1, 1, 1, 1, 1, 19, 50, 50, 62, 62, 107, 107] 107 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 401 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045599 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045599 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045599/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045599 Building REAL250005045600 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045600' /scratch/stefan/7916127/working/building/REAL250005045600 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045600 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045600/0 /scratch/stefan/7916127/working/building/REAL250005045600 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/736 `/scratch/stefan/7916127/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045600.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045600 none CC1=NC=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 154, 55, 55, 55, 27, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 154, 154, 55, 27, 27, 18, 18, 4, 1] 201 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]) total number of confs: 689 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045600 none CC1=NC=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 108, 126, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 9, 9, 47, 108, 108, 126, 126, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045600 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045600 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045600/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045600 Building REAL250005045601 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045601' /scratch/stefan/7916127/working/building/REAL250005045601 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045601 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045601/0 /scratch/stefan/7916127/working/building/REAL250005045601 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/737 `/scratch/stefan/7916127/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+](C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045601.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045601 none C[NH+](C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 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', '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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 22, 22, 22, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 22, 18, 18, 18, 18, 9, 1, 23, 23, 23, 23, 23, 23] 23 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, 39, 40]) total number of confs: 84 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: REAL250005045601 none C[NH+](C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 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', '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'] dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 1, 1, 5, 5, 5, 13, 17, 17, 17, 17, 23, 23, 23, 23, 23, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 13, 13, 17, 17, 17, 23, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [1, 35, 4, 5, 38, 39, 40, 19, 20, 21, 36, 37] set([0, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 89 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045601 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045601 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045601/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045601 Building REAL250005045602 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045602' /scratch/stefan/7916127/working/building/REAL250005045602 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045602 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045602/0 /scratch/stefan/7916127/working/building/REAL250005045602 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/738 `/scratch/stefan/7916127/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045602.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045602 none CC1CCCC1(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 140, 140, 103, 140, 103, 103, 48, 31, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 103, 48, 48, 31, 31, 11, 1] 140 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: 477 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: REAL250005045602 none CC1CCCC1(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 31, 53, 129, 129, 129, 140, 140, 140, 140, 140, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 31, 31, 53, 53, 129, 140] 140 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 487 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045602 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045602 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045602/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045602 Building REAL250005045603 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045603' /scratch/stefan/7916127/working/building/REAL250005045603 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045603 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045603/0 /scratch/stefan/7916127/working/building/REAL250005045603 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/739 `/scratch/stefan/7916127/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045603.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045603 none CC(F)(F)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 155, 201, 201, 79, 79, 79, 30, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 156, 156, 79, 30, 30, 18, 18, 4, 1] 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]) total number of confs: 886 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045603 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045603 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045603/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045603 Building REAL250005045604 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045604' /scratch/stefan/7916127/working/building/REAL250005045604 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045604 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045604/0 /scratch/stefan/7916127/working/building/REAL250005045604 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/740 `/scratch/stefan/7916127/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(CC(C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045604.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045604 none COC(CC(C)C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 92, 111, 115, 115, 115, 92, 92, 40, 23, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 115, 115, 115, 115, 115, 115, 115, 115, 115, 92, 40, 40, 23, 23, 4, 1] 115 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: 430 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045604 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045604 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045604/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045604 Building REAL250005045605 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045605' /scratch/stefan/7916127/working/building/REAL250005045605 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045605 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045605/0 /scratch/stefan/7916127/working/building/REAL250005045605 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/741 `/scratch/stefan/7916127/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045605.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045605 none CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 169, 69, 69, 69, 26, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 184, 184, 69, 26, 26, 16, 16, 4, 1, 169, 169, 169, 169] 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: 716 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: REAL250005045605 none CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 7, 7, 7, 39, 59, 164, 167, 167, 169, 169, 169, 169, 169, 1, 1, 7, 7, 7, 7, 7, 5, 5, 7, 39, 39, 59, 59, 167, 169, 1, 1, 1, 1] 201 rigid atoms, others: [35, 34, 3, 4, 37, 2, 18, 19, 36] set([0, 1, 5, 6, 7, 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: 582 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045605 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045605 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045605/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045605 Building REAL250005045606 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045606' /scratch/stefan/7916127/working/building/REAL250005045606 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045606 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045606/0 /scratch/stefan/7916127/working/building/REAL250005045606 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/742 `/scratch/stefan/7916127/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@]1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1) `REAL250005045606.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045606 none C[C@@]1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1 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.2', 'O.2', 'N.am', '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, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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, 129, 129, 129, 52, 36, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 183, 183, 129, 52, 52, 35, 35, 11, 1, 183, 183, 183, 183, 183] 183 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 596 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045606 none C[C@@]1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1 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.2', 'O.2', 'N.am', '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, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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: [1, 1, 1, 11, 11, 11, 50, 85, 169, 170, 169, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 2, 2, 2, 11, 50, 50, 85, 85, 170, 182, 1, 1, 1, 1, 1] 183 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045606 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045606 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045606/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045606 Building REAL250005045607 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045607' /scratch/stefan/7916127/working/building/REAL250005045607 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045607 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045607/0 /scratch/stefan/7916127/working/building/REAL250005045607 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/743 `/scratch/stefan/7916127/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045607.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045607 none CCC1=NOC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 140, 140, 140, 140, 140, 79, 79, 79, 27, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 140, 79, 27, 27, 16, 16, 4, 1] 201 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]) total number of confs: 719 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045607 none CCC1=NOC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 59, 78, 138, 138, 138, 140, 140, 140, 140, 140, 6, 6, 6, 5, 5, 1, 10, 59, 59, 78, 78, 138, 140] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045607 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045607 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045607/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045607 Building REAL250005045608 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045608' /scratch/stefan/7916127/working/building/REAL250005045608 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045608 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045608/0 /scratch/stefan/7916127/working/building/REAL250005045608 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/744 `/scratch/stefan/7916127/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1COCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045608.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045608 none CC1COCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 137, 137, 137, 61, 39, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 137, 61, 61, 39, 39, 11, 1] 167 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: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045608 none CC1COCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 45, 73, 152, 152, 152, 167, 167, 167, 167, 167, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 8, 45, 45, 73, 73, 152, 167] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045608 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045608 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045608/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045608 Building REAL250005045609 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045609' /scratch/stefan/7916127/working/building/REAL250005045609 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045609 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045609/0 /scratch/stefan/7916127/working/building/REAL250005045609 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/745 `/scratch/stefan/7916127/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1C) `REAL250005045609.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045609 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1C 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.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 123, 123, 123, 58, 36, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 123, 58, 58, 36, 36, 9, 1, 201, 201, 201, 201, 201] 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, 35]) total number of confs: 539 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045609 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CN1C 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.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 10, 10, 9, 48, 99, 191, 191, 191, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 10, 48, 48, 99, 99, 191, 201, 1, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35]) total number of confs: 742 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045609 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045609 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045609/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045609 Building REAL250005045610 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045610' /scratch/stefan/7916127/working/building/REAL250005045610 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045610 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045610/0 /scratch/stefan/7916127/working/building/REAL250005045610 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/746 `/scratch/stefan/7916127/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(Cl)N1) `REAL250005045610.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045610 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(Cl)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 16, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [11, 1, 11, 11, 41, 63, 113, 113, 113, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 11, 41, 41, 63, 63, 113, 119, 1, 1, 1] 119 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045610 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(Cl)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'Cl', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 16, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 41, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 93, 119, 119, 119, 119, 119, 93, 41, 41, 30, 30, 11, 1, 119, 119, 119] 119 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]) total number of confs: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045610 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045610 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045610/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045610 Building REAL250005045611 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045611' /scratch/stefan/7916127/working/building/REAL250005045611 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045611 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045611/0 /scratch/stefan/7916127/working/building/REAL250005045611 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/747 `/scratch/stefan/7916127/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045611.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045611 none COCC(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens 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, 192, 115, 72, 111, 147, 72, 72, 22, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 200, 200, 200, 192, 192, 115, 147, 147, 147, 72, 22, 22, 13, 13, 4, 1] 201 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: 908 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045611 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045611 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045611/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045611 Building REAL250005045612 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045612' /scratch/stefan/7916127/working/building/REAL250005045612 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045612 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045612/0 /scratch/stefan/7916127/working/building/REAL250005045612 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/748 `/scratch/stefan/7916127/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045612.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045612 none CC1(C)CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 123, 123, 123, 47, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 47, 47, 29, 29, 7, 1, 201, 201] 201 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: 656 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: REAL250005045612 none CC1(C)CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 64, 101, 195, 195, 195, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 64, 64, 101, 101, 195, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 20, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 722 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045612 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045612 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045612/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045612 Building REAL250005045613 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045613' /scratch/stefan/7916127/working/building/REAL250005045613 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045613 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045613/0 /scratch/stefan/7916127/working/building/REAL250005045613 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/749 `/scratch/stefan/7916127/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCCO1) `REAL250005045613.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045613 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCCO1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 6, 18, 18, 18, 56, 75, 143, 143, 143, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 6, 6, 6, 6, 18, 56, 56, 75, 75, 143, 143, 1, 1, 1, 1, 1, 1, 1] 143 rigid atoms, others: [32, 1, 34, 35, 36, 37, 38, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 521 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: REAL250005045613 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCCO1 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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 5, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [139, 78, 78, 78, 33, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 139, 143, 143, 143, 143, 139, 139, 139, 139, 78, 33, 33, 20, 20, 4, 1, 143, 143, 143, 143, 143, 143, 143] 143 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045613 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045613 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045613/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045613 Building REAL250005045614 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045614' /scratch/stefan/7916127/working/building/REAL250005045614 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045614 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045614/0 /scratch/stefan/7916127/working/building/REAL250005045614 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/750 `/scratch/stefan/7916127/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045614.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045614 none CCC[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 130, 130, 130, 130, 43, 130, 43, 43, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 189, 189, 130, 130, 43, 18, 18, 10, 10, 3, 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: 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: REAL250005045614 none CCC[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 70, 129, 129, 129, 130, 130, 130, 130, 130, 13, 13, 13, 13, 13, 7, 7, 1, 1, 12, 57, 57, 70, 70, 129, 130] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 511 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045614 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045614 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045614/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045614 Building REAL250005045615 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045615' /scratch/stefan/7916127/working/building/REAL250005045615 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045615 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045615/0 /scratch/stefan/7916127/working/building/REAL250005045615 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/751 `/scratch/stefan/7916127/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C12CC1CCCC2)C1=CC(=O)[N-]O1) `REAL250005045615.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045615 none O=C(NCCNC(=O)C12CC1CCCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 31, 54, 115, 115, 115, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 31, 31, 54, 54, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 545 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: REAL250005045615 none O=C(NCCNC(=O)C12CC1CCCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [192, 188, 83, 46, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 188, 201, 201, 201, 201, 201, 192, 83, 83, 46, 46, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 710 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045615 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045615 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045615/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045615 Building REAL250005045616 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045616' /scratch/stefan/7916127/working/building/REAL250005045616 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045616 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045616/0 /scratch/stefan/7916127/working/building/REAL250005045616 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/752 `/scratch/stefan/7916127/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045616.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045616 none CC(C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 103, 103, 103, 41, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 189, 189, 201, 201, 201, 201, 201, 201, 201, 103, 41, 41, 26, 26, 6, 1, 189, 189, 189, 189] 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: 683 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: REAL250005045616 none CC(C)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 1, 1, 6, 6, 6, 40, 67, 182, 184, 184, 189, 189, 189, 189, 189, 1, 1, 9, 9, 9, 9, 9, 9, 9, 6, 40, 40, 67, 67, 184, 189, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 3, 4, 37, 35, 18, 19, 36] set([0, 2, 5, 6, 7, 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: 658 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045616 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045616 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045616/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045616 Building REAL250005045617 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045617' /scratch/stefan/7916127/working/building/REAL250005045617 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045617 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045617/0 /scratch/stefan/7916127/working/building/REAL250005045617 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/753 `/scratch/stefan/7916127/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045617.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045617 none C=C1CC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 201, 114, 114, 53, 35, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 114, 53, 53, 35, 35, 10, 1, 201, 201] 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: 653 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: REAL250005045617 none C=C1CC(C)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 6, 47, 91, 187, 189, 187, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 6, 47, 47, 91, 91, 189, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 716 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045617 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045617 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045617/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045617 Building REAL250005045618 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045618' /scratch/stefan/7916127/working/building/REAL250005045618 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045618 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045618/0 /scratch/stefan/7916127/working/building/REAL250005045618 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/754 `/scratch/stefan/7916127/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(F)F) `REAL250005045618.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045618 none CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(F)F 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', 'F', 'F', '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, 15, 15, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 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, 29, 47, 29, 29, 13, 11, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 29, 13, 13, 11, 11, 4, 1, 47] 47 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]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045618 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045618 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045618/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045618 Building REAL250005045619 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045619' /scratch/stefan/7916127/working/building/REAL250005045619 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045619 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045619/0 /scratch/stefan/7916127/working/building/REAL250005045619 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/755 `/scratch/stefan/7916127/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=C1) `REAL250005045619.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045619 none CC1=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 151, 55, 55, 55, 24, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 151, 151, 55, 24, 24, 15, 15, 4, 1, 201, 201] 201 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: 652 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045619 none CC1=C(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=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', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'O.3', 'C.2', 'C.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 5, 38, 38, 38, 109, 125, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 5, 5, 38, 109, 109, 125, 125, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 33, 34, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 740 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045619 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045619 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045619/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045619 Building REAL250005045620 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045620' /scratch/stefan/7916127/working/building/REAL250005045620 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045620 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045620/0 /scratch/stefan/7916127/working/building/REAL250005045620 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/756 `/scratch/stefan/7916127/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=N1) `REAL250005045620.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045620 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.2', 'N.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 180, 120, 120, 120, 47, 27, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 180, 180, 180, 201, 201, 201, 201, 201, 120, 47, 47, 27, 27, 4, 1, 180] 201 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]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045620 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)OC=N1 NO_LONG_NAME dock atom types: ['C.3', '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', 'O.3', 'C.2', 'N.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 7, 7, 7, 41, 69, 166, 166, 166, 180, 180, 180, 180, 180, 1, 1, 1, 5, 5, 5, 5, 5, 7, 41, 41, 69, 69, 166, 180, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 594 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045620 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045620 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045620/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045620 Building REAL250005045621 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045621' /scratch/stefan/7916127/working/building/REAL250005045621 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045621 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045621/0 /scratch/stefan/7916127/working/building/REAL250005045621 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/757 `/scratch/stefan/7916127/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CF)CC1)C1=CC(=O)[N-]O1) `REAL250005045621.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045621 none O=C(NCCNC(=O)C1(CF)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 17, 26, 80, 80, 80, 177, 201, 177, 177, 1, 1, 1, 1, 1, 1, 4, 17, 17, 26, 26, 80, 201, 201, 177, 177, 177, 177, 1] 201 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 689 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: REAL250005045621 none O=C(NCCNC(=O)C1(CF)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 61, 43, 7, 7, 1, 7, 1, 1, 10, 1, 1, 167, 177, 177, 177, 177, 177, 167, 61, 61, 43, 43, 7, 10, 10, 1, 1, 1, 1, 177] 201 rigid atoms, others: [6, 8, 9, 11, 12, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 587 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045621 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045621 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045621/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045621 Building REAL250005045622 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045622' /scratch/stefan/7916127/working/building/REAL250005045622 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045622 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045622/0 /scratch/stefan/7916127/working/building/REAL250005045622 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/758 `/scratch/stefan/7916127/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2(CC2)C1)C1=CC(=O)[N-]O1) `REAL250005045622.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045622 none O=C(NCCNC(=O)C1CC2(CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [7, 1, 7, 7, 32, 49, 113, 113, 113, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 32, 32, 49, 49, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 647 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: REAL250005045622 none O=C(NCCNC(=O)C1CC2(CC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [193, 193, 112, 66, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 112, 112, 66, 66, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 742 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045622 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045622 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045622/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045622 Building REAL250005045623 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045623' /scratch/stefan/7916127/working/building/REAL250005045623 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045623 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045623/0 /scratch/stefan/7916127/working/building/REAL250005045623 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/759 `/scratch/stefan/7916127/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CO1) `REAL250005045623.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045623 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CO1 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.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 1, 13, 55, 55, 55, 124, 135, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 13, 13, 13, 55, 124, 124, 135, 135, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 33, 16, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) 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: REAL250005045623 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=CO1 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.2', 'C.2', 'C.2', 'C.2', 'O.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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 52, 52, 52, 24, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 136, 201, 201, 201, 201, 136, 136, 136, 136, 52, 24, 24, 15, 15, 4, 1, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34]) total number of confs: 639 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045623 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045623 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045623/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045623 Building REAL250005045624 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045624' /scratch/stefan/7916127/working/building/REAL250005045624 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045624 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045624/0 /scratch/stefan/7916127/working/building/REAL250005045624 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/760 `/scratch/stefan/7916127/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCNC1=O) `REAL250005045624.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045624 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCNC1=O 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', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [201, 136, 136, 136, 44, 27, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 136, 44, 44, 27, 27, 7, 1, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 650 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: REAL250005045624 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCNC1=O 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', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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, 7, 7, 7, 43, 75, 195, 196, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 7, 43, 43, 75, 75, 196, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 680 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045624 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045624 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045624/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045624 Building REAL250005045625 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045625' /scratch/stefan/7916127/working/building/REAL250005045625 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045625 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045625/0 /scratch/stefan/7916127/working/building/REAL250005045625 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/761 `/scratch/stefan/7916127/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC[N@@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045625.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045625 none CC1CCC[N@@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 17, 17, 4, 1] 28 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: 97 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: REAL250005045625 none CC1CCC[N@@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 17, 21, 28, 28, 28, 28, 28, 28, 28, 28, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 17, 17, 21, 21, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 123 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045625 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045625/1 /scratch/stefan/7916127/working/building/REAL250005045625 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/762 `/scratch/stefan/7916127/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC[N@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045625.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045625 none CC1CCC[N@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 10, 10, 4, 1] 17 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: 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: REAL250005045625 none CC1CCC[N@H+]1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 11, 14, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 11, 11, 14, 14, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045625 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045625 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045625/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045625/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045625 Building REAL250005045626 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045626' /scratch/stefan/7916127/working/building/REAL250005045626 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045626 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045626/0 /scratch/stefan/7916127/working/building/REAL250005045626 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/763 `/scratch/stefan/7916127/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CNC(=O)C=C1)C1=CC(=O)[N-]O1) `REAL250005045626.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045626 none O=C(NCCNC(=O)C1=CNC(=O)C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 32, 45, 81, 81, 81, 159, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 11, 32, 32, 45, 45, 81, 159, 159, 159, 159, 1] 159 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 426 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045626 none O=C(NCCNC(=O)C1=CNC(=O)C=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 3, 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: [147, 147, 77, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 147, 159, 159, 159, 159, 159, 147, 77, 77, 35, 35, 7, 1, 1, 1, 1, 159] 159 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 561 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045626 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045626 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045626/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045626 Building REAL250005045627 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045627' /scratch/stefan/7916127/working/building/REAL250005045627 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045627 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045627/0 /scratch/stefan/7916127/working/building/REAL250005045627 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/764 `/scratch/stefan/7916127/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045627.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045627 none CCCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 175, 135, 116, 99, 37, 37, 37, 31, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 191, 201, 201, 199, 198, 180, 180, 135, 135, 121, 121, 99, 99, 37, 31, 31, 22, 22, 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: 1032 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045627 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045627 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045627/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045627 Building REAL250005045628 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045628' /scratch/stefan/7916127/working/building/REAL250005045628 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045628 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045628/0 /scratch/stefan/7916127/working/building/REAL250005045628 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/765 `/scratch/stefan/7916127/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045628.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045628 none CC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 107, 191, 107, 107, 46, 27, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 191, 191, 191, 191, 107, 46, 46, 27, 27, 7, 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: 804 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045628 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045628 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045628/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045628 Building REAL250005045629 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045629' /scratch/stefan/7916127/working/building/REAL250005045629 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045629 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045629/0 /scratch/stefan/7916127/working/building/REAL250005045629 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/766 `/scratch/stefan/7916127/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045629.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045629 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 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, 115, 115, 115, 53, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 53, 53, 34, 34, 9, 1, 201, 201] 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]) total number of confs: 671 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: REAL250005045629 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.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, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 10, 10, 10, 52, 94, 190, 190, 190, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 52, 52, 94, 94, 190, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24, 25, 26, 27, 28, 37, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 727 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045629 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045629 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045629/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045629 Building REAL250005045630 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045630' /scratch/stefan/7916127/working/building/REAL250005045630 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045630 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045630/0 /scratch/stefan/7916127/working/building/REAL250005045630 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/767 `/scratch/stefan/7916127/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045630.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045630 none CCN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [185, 149, 149, 149, 149, 138, 138, 138, 61, 38, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 149, 185, 185, 185, 185, 185, 149, 149, 138, 61, 61, 38, 38, 7, 1] 185 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: 699 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045630 none CCN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 41, 128, 128, 128, 149, 149, 149, 149, 149, 1, 9, 9, 9, 9, 9, 1, 1, 5, 25, 25, 41, 41, 128, 149] 185 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 466 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045630 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045630 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045630/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045630 Building REAL250005045631 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045631' /scratch/stefan/7916127/working/building/REAL250005045631 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045631 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045631/0 /scratch/stefan/7916127/working/building/REAL250005045631 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/768 `/scratch/stefan/7916127/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C) `REAL250005045631.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045631 none CCOC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)C NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 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: [155, 151, 124, 90, 90, 90, 31, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 124, 194, 194, 155, 155, 155, 155, 155, 124, 90, 31, 31, 15, 15, 4, 1, 194, 194, 194, 194, 194, 194, 194] 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, 38, 39, 40]) total number of confs: 924 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045631 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045631 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045631/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045631 Building REAL250005045632 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045632' /scratch/stefan/7916127/working/building/REAL250005045632 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045632 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045632/0 /scratch/stefan/7916127/working/building/REAL250005045632 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/769 `/scratch/stefan/7916127/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045632.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045632 none C#CCOCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 135, 133, 133, 46, 46, 46, 17, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 133, 133, 133, 133, 46, 17, 17, 10, 10, 2, 1] 201 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]) total number of confs: 873 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045632 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045632 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045632/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045632 Building REAL250005045633 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045633' /scratch/stefan/7916127/working/building/REAL250005045633 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045633 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045633/0 /scratch/stefan/7916127/working/building/REAL250005045633 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/770 `/scratch/stefan/7916127/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045633.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045633 none C#CCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 161, 142, 79, 142, 79, 79, 26, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 142, 142, 142, 142, 79, 26, 26, 16, 16, 4, 1] 201 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]) total number of confs: 818 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045633 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045633 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045633/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045633 Building REAL250005045634 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045634' /scratch/stefan/7916127/working/building/REAL250005045634 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045634 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045634/0 /scratch/stefan/7916127/working/building/REAL250005045634 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/771 `/scratch/stefan/7916127/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCOCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045634.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045634 none O=C(CCOCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 113, 113, 116, 143, 201, 201, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 143, 143, 201, 201, 201, 201, 201, 51, 21, 21, 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: 817 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045634 none O=C(CCOCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 3, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 16, 16, 13, 6, 1, 1, 1, 1, 54, 54, 113, 115, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 16, 6, 6, 1, 1, 1, 1, 1, 54, 113, 113, 115, 115, 201, 201] 201 rigid atoms, others: [5, 6, 7, 8, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045634 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045634 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045634/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045634 Building REAL250005045635 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045635' /scratch/stefan/7916127/working/building/REAL250005045635 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045635 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045635/0 /scratch/stefan/7916127/working/building/REAL250005045635 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/772 `/scratch/stefan/7916127/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045635.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045635 none CC(C)(C(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 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] 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: [33, 17, 33, 33, 37, 37, 17, 17, 9, 7, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 37, 37, 17, 9, 9, 7, 7, 2, 1] 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]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045635 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045635 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045635/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045635 Building REAL250005045636 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045636' /scratch/stefan/7916127/working/building/REAL250005045636 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045636 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045636/0 /scratch/stefan/7916127/working/building/REAL250005045636 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/773 `/scratch/stefan/7916127/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005045636.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045636 none CC(C)[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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 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, 12, 13, 12, 12, 12, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 12, 12, 11, 11, 4, 1, 13, 13, 13, 13, 13, 13] 13 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, 41, 42]) total number of confs: 45 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045636 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045636 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045636/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045636 Building REAL250005045637 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045637' /scratch/stefan/7916127/working/building/REAL250005045637 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045637 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045637/0 /scratch/stefan/7916127/working/building/REAL250005045637 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/774 `/scratch/stefan/7916127/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)C=N1) `REAL250005045637.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045637 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)C=N1 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', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 119, 119, 119, 48, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 119, 48, 48, 34, 34, 9, 1, 180, 180, 180, 180] 180 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: 475 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: REAL250005045637 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)C=N1 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', 'N.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 46, 80, 174, 174, 174, 180, 180, 180, 180, 180, 1, 1, 1, 1, 2, 2, 2, 11, 46, 46, 80, 80, 174, 180, 2, 2, 2, 1] 180 rigid atoms, others: [0, 1, 2, 3, 34, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 655 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045637 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045637 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045637/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045637 Building REAL250005045638 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045638' /scratch/stefan/7916127/working/building/REAL250005045638 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045638 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045638/0 /scratch/stefan/7916127/working/building/REAL250005045638 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/775 `/scratch/stefan/7916127/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=CS1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045638.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045638 none O=C(CC1=CN=CS1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 129, 201, 201, 201, 201, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 129, 129, 201, 201, 51, 21, 21, 14, 14, 4, 1] 201 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]) total number of confs: 630 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045638 none O=C(CC1=CN=CS1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 27, 27, 109, 131, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 27, 109, 109, 131, 131, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 754 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045638 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045638 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045638/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045638 Building REAL250005045639 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045639' /scratch/stefan/7916127/working/building/REAL250005045639 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045639 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045639/0 /scratch/stefan/7916127/working/building/REAL250005045639 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/776 `/scratch/stefan/7916127/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)NN=C1)C1=CC(=O)[N-]O1) `REAL250005045639.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045639 none O=C(NCCNC(=O)C1=CC(=O)NN=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 41, 86, 86, 86, 171, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 9, 28, 28, 41, 41, 86, 171, 171, 171, 1] 171 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 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: REAL250005045639 none O=C(NCCNC(=O)C1=CC(=O)NN=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 68, 33, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 161, 171, 171, 171, 171, 171, 161, 68, 68, 33, 33, 7, 1, 1, 1, 171] 171 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045639 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045639 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045639/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045639 Building REAL250005045640 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045640' /scratch/stefan/7916127/working/building/REAL250005045640 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045640 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045640/0 /scratch/stefan/7916127/working/building/REAL250005045640 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/777 `/scratch/stefan/7916127/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC(=O)N1) `REAL250005045640.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045640 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 117, 117, 117, 47, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 117, 47, 47, 32, 32, 9, 1, 201, 201] 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]) total number of confs: 497 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: REAL250005045640 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC(=O)N1 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', 'N.am', 'C.2', 'O.2', 'N.am', '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, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 58, 112, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 10, 58, 58, 112, 112, 195, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 32, 17, 18, 19, 20, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 771 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045640 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045640 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045640/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045640 Building REAL250005045641 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045641' /scratch/stefan/7916127/working/building/REAL250005045641 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045641 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045641/0 /scratch/stefan/7916127/working/building/REAL250005045641 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/778 `/scratch/stefan/7916127/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(C2CC2)CC1)C1=CC(=O)[N-]O1) `REAL250005045641.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045641 none O=C(NCCNC(=O)C1(C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [201, 201, 121, 95, 23, 23, 9, 23, 1, 1, 1, 1, 9, 9, 201, 201, 201, 201, 201, 201, 201, 121, 121, 95, 95, 23, 1, 1, 1, 1, 1, 9, 9, 9, 9, 201] 201 rigid atoms, others: [8, 9, 10, 11, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35]) total number of confs: 758 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045641 none O=C(NCCNC(=O)C1(C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [4, 1, 4, 4, 16, 28, 67, 67, 67, 122, 201, 201, 122, 122, 1, 1, 1, 1, 1, 1, 4, 16, 16, 28, 28, 67, 201, 201, 201, 201, 201, 122, 122, 122, 122, 1] 201 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 686 number of broken/clashed sets: 13 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045641 none O=C(NCCNC(=O)C1(C2CC2)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [114, 112, 42, 30, 6, 6, 1, 6, 1, 1, 9, 9, 1, 1, 112, 122, 122, 122, 122, 122, 114, 42, 42, 30, 30, 6, 9, 9, 9, 9, 9, 1, 1, 1, 1, 122] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 12, 13, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 415 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045641 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045641 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045641/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045641 Building REAL250005045642 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045642' /scratch/stefan/7916127/working/building/REAL250005045642 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045642 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045642/0 /scratch/stefan/7916127/working/building/REAL250005045642 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/779 `/scratch/stefan/7916127/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045642.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045642 none COC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 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, 113, 113, 113, 36, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 113, 36, 36, 25, 25, 7, 1, 201, 201] 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: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045642 none COC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 11, 11, 11, 60, 99, 195, 197, 195, 201, 201, 201, 201, 201, 1, 6, 6, 6, 1, 1, 1, 1, 11, 60, 60, 99, 99, 197, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 35, 34, 19, 23, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 727 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045642 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045642 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045642/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045642 Building REAL250005045643 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045643' /scratch/stefan/7916127/working/building/REAL250005045643 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045643 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045643/0 /scratch/stefan/7916127/working/building/REAL250005045643 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/780 `/scratch/stefan/7916127/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1CCCC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045643.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045643 none O=C(NCCNC(=O)[C@H]1CCCC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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: [12, 1, 12, 12, 31, 43, 111, 111, 111, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 12, 31, 31, 43, 43, 111, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 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, 33, 34]) total number of confs: 637 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: REAL250005045643 none O=C(NCCNC(=O)[C@H]1CCCC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', '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, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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: [193, 193, 110, 82, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 110, 110, 82, 82, 13, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 712 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045643 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045643 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045643/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045643 Building REAL250005045644 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045644' /scratch/stefan/7916127/working/building/REAL250005045644 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045644 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045644/0 /scratch/stefan/7916127/working/building/REAL250005045644 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/781 `/scratch/stefan/7916127/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@H+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045644.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045644 none CC1CC[N@H+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 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, 22, 24, 20, 20, 20, 15, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 22, 20, 15, 15, 13, 13, 4, 1, 24, 24] 24 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, 39, 40]) 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: REAL250005045644 none CC1CC[N@H+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 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, 1, 5, 12, 12, 12, 17, 20, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 12, 17, 17, 20, 20, 24, 24, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045644 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045644/1 /scratch/stefan/7916127/working/building/REAL250005045644 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/782 `/scratch/stefan/7916127/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC[N@@H+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045644.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045644 none CC1CC[N@@H+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 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, 21, 24, 18, 18, 18, 13, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 21, 21, 18, 13, 13, 11, 11, 3, 1, 24, 24] 24 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, 39, 40]) 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: REAL250005045644 none CC1CC[N@@H+](CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', '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', '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, 9, 6, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 6, 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, 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, 1, 5, 12, 12, 12, 16, 19, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 5, 12, 16, 16, 19, 19, 24, 24, 1, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045644 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045644 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045644/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045644/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045644 Building REAL250005045645 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045645' /scratch/stefan/7916127/working/building/REAL250005045645 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045645 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045645/0 /scratch/stefan/7916127/working/building/REAL250005045645 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/783 `/scratch/stefan/7916127/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)[C@@H]1C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045645.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045645 none NC(=O)[C@@H]1C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [125, 115, 125, 115, 115, 115, 81, 115, 81, 81, 32, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 125, 125, 115, 115, 81, 32, 32, 20, 20, 6, 1] 125 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: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045645 none NC(=O)[C@@H]1C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 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 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 37, 59, 104, 104, 104, 115, 115, 115, 115, 115, 8, 8, 1, 1, 8, 37, 37, 59, 59, 104, 115] 125 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 416 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045645 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045645 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045645/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045645 Building REAL250005045646 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045646' /scratch/stefan/7916127/working/building/REAL250005045646 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045646 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045646/0 /scratch/stefan/7916127/working/building/REAL250005045646 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/784 `/scratch/stefan/7916127/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005045646.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045646 none CC[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', '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', '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'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 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, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 18, 19, 18, 18, 16, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 16, 16, 15, 15, 4, 1, 19, 19, 19, 19, 19, 19] 19 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, 39]) total number of confs: 71 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045646 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045646 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045646/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045646 Building REAL250005045647 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045647' /scratch/stefan/7916127/working/building/REAL250005045647 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045647 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045647/0 /scratch/stefan/7916127/working/building/REAL250005045647 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/785 `/scratch/stefan/7916127/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(F)F) `REAL250005045647.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045647 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(F)F 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', 'F', 'F', '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, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 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: [22, 15, 15, 15, 7, 7, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 22, 27, 27, 27, 22, 22, 22, 22, 15, 7, 7, 7, 7, 4, 1, 27, 27, 27] 27 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045647 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045647 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045647/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045647 Building REAL250005045648 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045648' /scratch/stefan/7916127/working/building/REAL250005045648 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045648 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045648/0 /scratch/stefan/7916127/working/building/REAL250005045648 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/786 `/scratch/stefan/7916127/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045648.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045648 none CC1=NC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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, 151, 95, 95, 95, 41, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 151, 151, 151, 151, 151, 151, 151, 95, 41, 41, 32, 32, 11, 1, 151] 151 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]) total number of confs: 406 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: REAL250005045648 none CC1=NC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 54, 78, 137, 139, 137, 151, 151, 151, 151, 151, 1, 2, 2, 2, 2, 2, 2, 12, 54, 54, 78, 78, 139, 151, 1] 151 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 20] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 558 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045648 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045648 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045648/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045648 Building REAL250005045649 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045649' /scratch/stefan/7916127/working/building/REAL250005045649 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045649 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045649/0 /scratch/stefan/7916127/working/building/REAL250005045649 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/787 `/scratch/stefan/7916127/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1) `REAL250005045649.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045649 none CC1=NN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 183, 102, 102, 102, 32, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 183, 183, 102, 32, 32, 20, 20, 4, 1, 201, 201] 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]) total number of confs: 716 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045649 none CC1=NN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 31, 31, 31, 88, 131, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 8, 8, 31, 88, 88, 131, 131, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 34, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 769 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045649 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045649 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045649/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045649 Building REAL250005045650 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045650' /scratch/stefan/7916127/working/building/REAL250005045650 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045650 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045650/0 /scratch/stefan/7916127/working/building/REAL250005045650 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/788 `/scratch/stefan/7916127/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045650.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045650 none O=C(CCC1=NNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 138, 169, 201, 201, 201, 201, 29, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 138, 138, 169, 169, 201, 201, 57, 29, 29, 20, 20, 4, 1] 201 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]) total number of confs: 776 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045650 none O=C(CCC1=NNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 12, 6, 1, 1, 1, 1, 1, 1, 60, 60, 143, 158, 201, 201, 201, 201, 201, 201, 201, 201, 12, 12, 6, 6, 1, 1, 60, 143, 143, 158, 158, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 783 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045650 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045650/1 /scratch/stefan/7916127/working/building/REAL250005045650 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/789 `/scratch/stefan/7916127/working/3D/789' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNN=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045650.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045650 none O=C(CCC1=CNN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 150, 171, 201, 201, 201, 201, 33, 24, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 151, 151, 171, 171, 201, 201, 75, 33, 33, 24, 24, 7, 1] 201 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]) total number of confs: 749 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045650 none O=C(CCC1=CNN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 14, 6, 1, 1, 1, 1, 1, 1, 61, 61, 133, 161, 195, 195, 195, 201, 201, 201, 201, 201, 14, 14, 6, 6, 1, 1, 61, 137, 137, 160, 160, 195, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 812 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045650 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045650 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045650/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045650/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045650 Building REAL250005045651 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045651' /scratch/stefan/7916127/working/building/REAL250005045651 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045651 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045651/0 /scratch/stefan/7916127/working/building/REAL250005045651 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/790 `/scratch/stefan/7916127/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CF)CCC1)C1=CC(=O)[N-]O1) `REAL250005045651.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045651 none O=C(NCCNC(=O)C1(CF)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 3, 17, 26, 74, 74, 74, 176, 201, 176, 176, 176, 1, 1, 1, 1, 1, 1, 4, 17, 17, 26, 26, 74, 201, 201, 176, 176, 176, 176, 176, 176, 1] 201 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 699 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: REAL250005045651 none O=C(NCCNC(=O)C1(CF)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 15, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 164, 61, 40, 6, 6, 1, 6, 1, 1, 10, 1, 1, 1, 165, 176, 176, 176, 176, 176, 165, 61, 61, 40, 40, 6, 10, 10, 1, 1, 1, 1, 1, 1, 176] 201 rigid atoms, others: [32, 33, 6, 8, 9, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34]) total number of confs: 607 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045651 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045651 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045651/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045651 Building REAL250005045652 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045652' /scratch/stefan/7916127/working/building/REAL250005045652 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045652 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045652/0 /scratch/stefan/7916127/working/building/REAL250005045652 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/791 `/scratch/stefan/7916127/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C[C@@H]1OCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045652.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045652 none C=C[C@@H]1OCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 83, 201, 83, 83, 30, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 83, 30, 30, 18, 18, 4, 1] 201 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: 622 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045652 none C=C[C@@H]1OCC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 54, 83, 187, 191, 187, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 9, 54, 54, 83, 83, 191, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 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: 709 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045652 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045652 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045652/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045652 Building REAL250005045653 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045653' /scratch/stefan/7916127/working/building/REAL250005045653 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045653 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045653/0 /scratch/stefan/7916127/working/building/REAL250005045653 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/792 `/scratch/stefan/7916127/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045653.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045653 none CC(C)C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', '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, 7, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 201, 148, 148, 148, 148, 48, 148, 48, 48, 20, 12, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 198, 198, 148, 148, 48, 20, 20, 12, 12, 3, 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: 727 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: REAL250005045653 none CC(C)C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', '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, 7, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 6, 8, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 73, 143, 145, 145, 148, 148, 148, 148, 148, 8, 8, 8, 8, 8, 8, 8, 6, 6, 1, 1, 12, 59, 59, 73, 73, 145, 148] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 556 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045653 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045653 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045653/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045653 Building REAL250005045654 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045654' /scratch/stefan/7916127/working/building/REAL250005045654 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045654 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045654/0 /scratch/stefan/7916127/working/building/REAL250005045654 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/793 `/scratch/stefan/7916127/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045654.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045654 none CC[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 163, 163, 163, 163, 74, 163, 74, 74, 27, 17, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 163, 163, 74, 27, 27, 16, 16, 4, 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: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045654 none CC[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 59, 76, 162, 162, 162, 163, 163, 163, 163, 163, 3, 3, 3, 3, 3, 1, 1, 13, 59, 59, 76, 76, 162, 163] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27] set([0, 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: 572 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045654 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045654 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045654/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045654 Building REAL250005045655 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045655' /scratch/stefan/7916127/working/building/REAL250005045655 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045655 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045655/0 /scratch/stefan/7916127/working/building/REAL250005045655 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/794 `/scratch/stefan/7916127/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2)C1=CC(=O)[N-]O1) `REAL250005045655.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045655 none O=C(NCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 30, 45, 107, 107, 107, 161, 161, 161, 161, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 7, 29, 29, 45, 45, 107, 161, 161, 161, 161, 161, 161, 1] 161 rigid atoms, others: [1, 36, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 536 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: REAL250005045655 none O=C(NCCNC(=O)[C@@H]1C[C@H]2CC[C@@H]1O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 7, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [157, 155, 94, 65, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 155, 161, 161, 161, 161, 161, 157, 94, 94, 65, 65, 12, 1, 1, 1, 1, 1, 1, 161] 161 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 608 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045655 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045655 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045655/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045655 Building REAL250005045656 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045656' /scratch/stefan/7916127/working/building/REAL250005045656 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045656 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045656/0 /scratch/stefan/7916127/working/building/REAL250005045656 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/795 `/scratch/stefan/7916127/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(NC(C)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045656.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045656 none CCC(NC(C)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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', '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, 5, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 7, 6, 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] 0 hydrogens need rotated 131 conformations in input total number of sets (complete confs): 131 using faster count positions algorithm for large data unique positions, atoms: [127, 116, 73, 116, 123, 123, 123, 73, 73, 29, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 116, 123, 123, 123, 123, 73, 29, 29, 17, 17, 4, 1] 131 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: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045656 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045656 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045656/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045656 Building REAL250005045657 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045657' /scratch/stefan/7916127/working/building/REAL250005045657 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045657 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045657/0 /scratch/stefan/7916127/working/building/REAL250005045657 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/796 `/scratch/stefan/7916127/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045657.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045657 none CC(C)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 193, 162, 147, 152, 50, 50, 50, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 194, 201, 201, 201, 201, 193, 193, 186, 186, 152, 152, 50, 19, 19, 12, 12, 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: 1394 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045657 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045657 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045657/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045657 Building REAL250005045658 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045658' /scratch/stefan/7916127/working/building/REAL250005045658 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045658 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045658/0 /scratch/stefan/7916127/working/building/REAL250005045658 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/797 `/scratch/stefan/7916127/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045658.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045658 none O=C(CN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 170, 201, 201, 201, 201, 40, 25, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 108, 40, 40, 25, 25, 4, 1] 201 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]) total number of confs: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045658 none O=C(CN1C=NC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 8, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 35, 35, 97, 134, 201, 201, 201, 201, 201, 201, 201, 201, 9, 9, 1, 1, 35, 97, 97, 134, 134, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045658 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045658 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045658/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045658 Building REAL250005045659 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045659' /scratch/stefan/7916127/working/building/REAL250005045659 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045659 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045659/0 /scratch/stefan/7916127/working/building/REAL250005045659 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/798 `/scratch/stefan/7916127/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045659.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045659 none NC(=O)NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 4, 7, 7, 7, 6, 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] 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: [193, 193, 192, 158, 146, 62, 62, 62, 30, 19, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 193, 193, 192, 159, 159, 147, 147, 62, 30, 30, 19, 19, 6, 1] 193 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]) total number of confs: 794 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045659 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045659 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045659/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045659 Building REAL250005045660 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045660' /scratch/stefan/7916127/working/building/REAL250005045660 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045660 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045660/0 /scratch/stefan/7916127/working/building/REAL250005045660 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/799 `/scratch/stefan/7916127/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045660.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045660 none CC1=CN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 175, 201, 201, 118, 118, 118, 48, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 118, 48, 48, 34, 34, 11, 1] 201 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]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045660 none CC1=CN=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 63, 105, 193, 193, 193, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 10, 63, 63, 105, 105, 193, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045660 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045660 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045660/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045660 Building REAL250005045661 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045661' /scratch/stefan/7916127/working/building/REAL250005045661 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045661 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045661/0 /scratch/stefan/7916127/working/building/REAL250005045661 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/800 `/scratch/stefan/7916127/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC1(F)F)C1=CC(=O)[N-]O1) `REAL250005045661.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045661 none O=C(NCCNC(=O)C1CCC1(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 7, 31, 49, 121, 121, 121, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 31, 31, 49, 49, 121, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 663 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: REAL250005045661 none O=C(NCCNC(=O)C1CCC1(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 197, 114, 72, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 198, 201, 201, 201, 201, 201, 198, 114, 114, 72, 72, 13, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31]) total number of confs: 754 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045661 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045661 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045661/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045661 Building REAL250005045662 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045662' /scratch/stefan/7916127/working/building/REAL250005045662 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045662 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045662/0 /scratch/stefan/7916127/working/building/REAL250005045662 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/801 `/scratch/stefan/7916127/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NSC=C1) `REAL250005045662.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045662 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 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, 5, 20, 31, 66, 66, 66, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 5, 20, 20, 31, 31, 66, 70, 1, 1] 70 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) 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: REAL250005045662 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NSC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 14, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [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] 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, 37, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 37, 37, 22, 22, 9, 1, 70, 70] 70 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045662 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045662 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045662/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045662 Building REAL250005045663 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045663' /scratch/stefan/7916127/working/building/REAL250005045663 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045663 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045663/0 /scratch/stefan/7916127/working/building/REAL250005045663 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/802 `/scratch/stefan/7916127/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005045663.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045663 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 21, 21, 21, 89, 120, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 3, 3, 3, 3, 21, 89, 89, 120, 120, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 34, 35, 36, 37, 33, 16, 17, 18, 19, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 747 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: REAL250005045663 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 107, 107, 107, 43, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 107, 43, 43, 26, 26, 4, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 802 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045663 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045663 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045663/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045663 Building REAL250005045664 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045664' /scratch/stefan/7916127/working/building/REAL250005045664 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045664 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045664/0 /scratch/stefan/7916127/working/building/REAL250005045664 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/803 `/scratch/stefan/7916127/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1C=CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045664.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045664 none O=C(CC1C=CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 162, 201, 201, 201, 201, 201, 26, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 162, 162, 201, 201, 201, 201, 201, 201, 201, 201, 201, 65, 26, 26, 18, 18, 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: 748 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045664 none O=C(CC1C=CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 8, 1, 1, 1, 1, 1, 1, 1, 34, 34, 97, 124, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 97, 97, 124, 124, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 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/7916127/working/building/REAL250005045664 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045664 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045664/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045664 Building REAL250005045665 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045665' /scratch/stefan/7916127/working/building/REAL250005045665 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045665 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045665/0 /scratch/stefan/7916127/working/building/REAL250005045665 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/804 `/scratch/stefan/7916127/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045665.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045665 none CCOCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need 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, 172, 128, 73, 73, 73, 31, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 128, 128, 201, 201, 201, 201, 201, 172, 172, 73, 31, 31, 19, 19, 4, 1, 128, 128, 128, 128] 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: 714 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045665 none CCOCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 26, 8, 1, 1, 1, 7, 7, 7, 37, 52, 115, 115, 115, 128, 128, 128, 128, 128, 1, 1, 38, 38, 38, 38, 38, 8, 8, 7, 37, 37, 52, 52, 115, 128, 1, 1, 1, 1] 201 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: 542 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045665 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045665 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045665/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045665 Building REAL250005045666 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045666' /scratch/stefan/7916127/working/building/REAL250005045666 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045666 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045666/0 /scratch/stefan/7916127/working/building/REAL250005045666 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/805 `/scratch/stefan/7916127/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2C=CC1O2)C1=CC(=O)[N-]O1) `REAL250005045666.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045666 none O=C(NCCNC(=O)C1CC2C=CC1O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 34, 49, 118, 118, 118, 171, 171, 171, 171, 171, 171, 1, 1, 1, 1, 1, 1, 10, 34, 34, 49, 49, 118, 171, 171, 171, 171, 171, 171, 171, 1] 171 rigid atoms, others: [1, 34, 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]) total number of confs: 563 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: REAL250005045666 none O=C(NCCNC(=O)C1CC2C=CC1O2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 98, 64, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 163, 171, 171, 171, 171, 171, 163, 98, 98, 64, 64, 12, 1, 1, 1, 1, 1, 1, 1, 171] 171 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 635 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045666 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045666 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045666/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045666 Building REAL250005045667 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045667' /scratch/stefan/7916127/working/building/REAL250005045667 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045667 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045667/0 /scratch/stefan/7916127/working/building/REAL250005045667 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/806 `/scratch/stefan/7916127/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045667.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045667 none COC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 104, 104, 104, 38, 24, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 38, 38, 24, 24, 5, 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: 633 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: REAL250005045667 none COC1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 56, 93, 195, 199, 195, 201, 201, 201, 201, 201, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 56, 56, 93, 93, 199, 201] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 732 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045667 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045667 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045667/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045667 Building REAL250005045668 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045668' /scratch/stefan/7916127/working/building/REAL250005045668 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045668 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045668/0 /scratch/stefan/7916127/working/building/REAL250005045668 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/807 `/scratch/stefan/7916127/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CO1) `REAL250005045668.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045668 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CO1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 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, 201, 201, 124, 124, 124, 49, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 49, 49, 31, 31, 10, 1, 201, 201] 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]) total number of confs: 649 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: REAL250005045668 none CC1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CO1 NO_LONG_NAME dock atom types: ['C.3', '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', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 52, 94, 189, 190, 189, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 10, 52, 52, 94, 94, 190, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 23, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 724 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045668 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045668 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045668/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045668 Building REAL250005045669 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045669' /scratch/stefan/7916127/working/building/REAL250005045669 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045669 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045669/0 /scratch/stefan/7916127/working/building/REAL250005045669 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/808 `/scratch/stefan/7916127/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCC2CC21)C1=CC(=O)[N-]O1) `REAL250005045669.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045669 none O=C(NCCNC(=O)C1CCCC2CC21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [8, 1, 8, 8, 25, 39, 108, 108, 108, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 25, 25, 39, 39, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 626 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: REAL250005045669 none O=C(NCCNC(=O)C1CCCC2CC21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [199, 199, 122, 80, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 201, 199, 122, 122, 80, 80, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 772 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045669 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045669 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045669/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045669 Building REAL250005045670 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045670' /scratch/stefan/7916127/working/building/REAL250005045670 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045670 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045670/0 /scratch/stefan/7916127/working/building/REAL250005045670 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/809 `/scratch/stefan/7916127/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC2CC21)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045670.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045670 none O=C(CC1CCC2CC21)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 64, 64, 168, 201, 201, 201, 201, 201, 26, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 64, 26, 26, 17, 17, 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: 768 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: REAL250005045670 none O=C(CC1CCC2CC21)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 7, 1, 1, 1, 1, 1, 1, 1, 37, 37, 112, 131, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 112, 112, 131, 131, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 725 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045670 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045670 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045670/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045670 Building REAL250005045671 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045671' /scratch/stefan/7916127/working/building/REAL250005045671 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045671 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045671/0 /scratch/stefan/7916127/working/building/REAL250005045671 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/810 `/scratch/stefan/7916127/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC2CC2C1)C1=CC(=O)[N-]O1) `REAL250005045671.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045671 none O=C(NCCNC(=O)C1CCC2CC2C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 30, 49, 119, 119, 119, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 30, 30, 49, 49, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 655 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: REAL250005045671 none O=C(NCCNC(=O)C1CCC2CC2C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [196, 194, 110, 70, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 194, 201, 201, 201, 201, 201, 196, 110, 110, 70, 70, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 745 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045671 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045671 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045671/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045671 Building REAL250005045672 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045672' /scratch/stefan/7916127/working/building/REAL250005045672 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045672 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045672/0 /scratch/stefan/7916127/working/building/REAL250005045672 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/811 `/scratch/stefan/7916127/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)C(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045672.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045672 none CCC(C)C(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 12, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 178, 104, 178, 75, 104, 111, 75, 75, 27, 14, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 199, 200, 200, 200, 200, 178, 178, 178, 178, 104, 111, 111, 111, 75, 27, 27, 14, 14, 3, 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: 920 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045672 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045672 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045672/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045672 Building REAL250005045673 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045673' /scratch/stefan/7916127/working/building/REAL250005045673 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045673 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045673/0 /scratch/stefan/7916127/working/building/REAL250005045673 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/812 `/scratch/stefan/7916127/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045673.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045673 none COC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 100, 100, 100, 33, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 33, 33, 23, 23, 7, 1, 201, 201] 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, 37, 38]) total number of confs: 612 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: REAL250005045673 none COC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 10, 10, 10, 55, 87, 195, 195, 195, 201, 201, 201, 201, 201, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 10, 55, 55, 87, 87, 195, 201, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 38, 20, 24, 25, 26, 27, 28, 29, 37] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 714 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045673 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045673 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045673/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045673 Building REAL250005045674 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045674' /scratch/stefan/7916127/working/building/REAL250005045674 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045674 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045674/0 /scratch/stefan/7916127/working/building/REAL250005045674 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/813 `/scratch/stefan/7916127/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(CC)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045674.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045674 none CCC(CC)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 150, 137, 145, 201, 55, 137, 55, 55, 29, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 152, 201, 194, 201, 201, 201, 137, 137, 137, 137, 55, 29, 29, 21, 21, 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: 1272 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045674 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045674 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045674/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045674 Building REAL250005045675 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045675' /scratch/stefan/7916127/working/building/REAL250005045675 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045675 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045675/0 /scratch/stefan/7916127/working/building/REAL250005045675 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/814 `/scratch/stefan/7916127/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC12CC2)C1=CC(=O)[N-]O1) `REAL250005045675.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045675 none O=C(NCCNC(=O)C1CC12CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens 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, 26, 40, 107, 107, 107, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 6, 26, 26, 40, 40, 107, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 642 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: REAL250005045675 none O=C(NCCNC(=O)C1CC12CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need 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, 116, 73, 13, 13, 1, 13, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 201, 201, 116, 116, 73, 73, 13, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 769 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045675 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045675 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045675/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045675 Building REAL250005045676 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045676' /scratch/stefan/7916127/working/building/REAL250005045676 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045676 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045676/0 /scratch/stefan/7916127/working/building/REAL250005045676 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/815 `/scratch/stefan/7916127/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045676.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045676 none O=C(CC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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] 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: [71, 71, 71, 154, 175, 175, 175, 175, 28, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 154, 154, 175, 175, 175, 71, 28, 28, 17, 17, 4, 1] 175 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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045676 none O=C(CC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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] 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: [25, 7, 1, 1, 1, 1, 1, 1, 25, 25, 79, 99, 175, 175, 175, 175, 175, 175, 175, 175, 7, 7, 1, 1, 1, 25, 79, 79, 99, 99, 175, 175] 175 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 676 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045676 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045676/1 /scratch/stefan/7916127/working/building/REAL250005045676 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/816 `/scratch/stefan/7916127/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045676.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045676/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045676 none O=C(CC1=CN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 146, 201, 201, 201, 201, 25, 16, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 146, 146, 201, 201, 201, 67, 25, 25, 16, 16, 6, 1] 201 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]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045676 none O=C(CC1=CN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 4, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 5, 1, 1, 1, 1, 1, 1, 34, 34, 118, 133, 197, 197, 197, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 34, 118, 118, 133, 133, 197, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 737 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045676 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045676 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045676/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045676/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045676 Building REAL250005045677 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045677' /scratch/stefan/7916127/working/building/REAL250005045677 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045677 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045677/0 /scratch/stefan/7916127/working/building/REAL250005045677 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/817 `/scratch/stefan/7916127/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045677.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045677 none C=CCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 149, 67, 147, 147, 67, 67, 33, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 147, 149, 149, 149, 147, 67, 33, 33, 20, 20, 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: 933 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045677 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045677 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045677/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045677 Building REAL250005045678 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045678' /scratch/stefan/7916127/working/building/REAL250005045678 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045678 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045678/0 /scratch/stefan/7916127/working/building/REAL250005045678 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/818 `/scratch/stefan/7916127/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)N1) `REAL250005045678.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045678 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 101, 101, 101, 43, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 101, 43, 43, 26, 26, 7, 1, 162, 162, 162, 162] 162 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: 440 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: REAL250005045678 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C(C)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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.2', 'C.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 11, 11, 11, 60, 84, 158, 158, 158, 162, 162, 162, 162, 162, 1, 1, 1, 2, 2, 2, 1, 12, 59, 59, 84, 84, 158, 162, 2, 2, 2, 1] 162 rigid atoms, others: [0, 1, 2, 3, 4, 35, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 591 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045678 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045678 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045678/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045678 Building REAL250005045679 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045679' /scratch/stefan/7916127/working/building/REAL250005045679 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045679 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045679/0 /scratch/stefan/7916127/working/building/REAL250005045679 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/819 `/scratch/stefan/7916127/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC12CCC2)C1=CC(=O)[N-]O1) `REAL250005045679.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045679 none O=C(NCCNC(=O)C1CC12CCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [7, 1, 7, 7, 29, 44, 120, 120, 120, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 29, 29, 44, 44, 120, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 640 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045679 none O=C(NCCNC(=O)C1CC12CCC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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: [200, 200, 108, 67, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 201, 200, 108, 108, 67, 67, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 745 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045679 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045679 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045679/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045679 Building REAL250005045680 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045680' /scratch/stefan/7916127/working/building/REAL250005045680 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045680 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045680/0 /scratch/stefan/7916127/working/building/REAL250005045680 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/820 `/scratch/stefan/7916127/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=NN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045680.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045680 none CC1=CC=NN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 187, 104, 104, 104, 38, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 187, 187, 104, 38, 38, 24, 24, 6, 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: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045680 none CC1=CC=NN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 29, 29, 29, 76, 119, 199, 199, 199, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 7, 7, 29, 76, 76, 119, 119, 199, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([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]) total number of confs: 760 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045680 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045680 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045680/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045680 Building REAL250005045681 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045681' /scratch/stefan/7916127/working/building/REAL250005045681 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045681 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045681/0 /scratch/stefan/7916127/working/building/REAL250005045681 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/821 `/scratch/stefan/7916127/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045681.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045681 none CC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 101, 101, 101, 47, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 148, 148, 148, 148, 148, 148, 101, 47, 47, 32, 32, 9, 1] 148 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]) total number of confs: 414 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045681 none CC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 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] 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, 1, 12, 12, 12, 54, 81, 144, 144, 144, 148, 148, 148, 148, 148, 2, 2, 2, 1, 1, 1, 12, 54, 54, 81, 81, 144, 148] 148 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045681 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045681 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045681/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045681 Building REAL250005045682 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045682' /scratch/stefan/7916127/working/building/REAL250005045682 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045682 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045682/0 /scratch/stefan/7916127/working/building/REAL250005045682 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/822 `/scratch/stefan/7916127/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045682.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045682 none CN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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, 67, 65, 65, 65, 37, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 65, 37, 37, 26, 26, 9, 1] 67 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]) 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: REAL250005045682 none CN1C=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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, 5, 21, 38, 61, 61, 61, 67, 67, 67, 67, 67, 1, 2, 2, 2, 1, 1, 5, 21, 21, 38, 38, 61, 67] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 25, 26, 27, 28, 29, 30, 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/7916127/working/building/REAL250005045682 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045682 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045682/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045682 Building REAL250005045683 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045683' /scratch/stefan/7916127/working/building/REAL250005045683 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045683 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045683/0 /scratch/stefan/7916127/working/building/REAL250005045683 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/823 `/scratch/stefan/7916127/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045683.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045683 none CC1=NC=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 160, 59, 59, 59, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 160, 160, 59, 23, 23, 14, 14, 4, 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: 667 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045683 none CC1=NC=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 35, 35, 35, 98, 116, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 8, 8, 35, 98, 98, 116, 116, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([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]) total number of confs: 721 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045683 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045683/1 /scratch/stefan/7916127/working/building/REAL250005045683 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/824 `/scratch/stefan/7916127/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=[NH+]C=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045683.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045683 none CC1=[NH+]C=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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] 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, 42, 42, 38, 23, 23, 23, 15, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 38, 38, 23, 15, 15, 13, 13, 4, 1] 42 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: 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: REAL250005045683 none CC1=[NH+]C=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 19, 19, 19, 27, 33, 42, 42, 42, 42, 42, 42, 42, 42, 2, 2, 2, 1, 1, 5, 5, 19, 27, 27, 33, 33, 42, 42] 42 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045683 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045683 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045683/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045683/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045683 Building REAL250005045684 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045684' /scratch/stefan/7916127/working/building/REAL250005045684 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045684 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045684/0 /scratch/stefan/7916127/working/building/REAL250005045684 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/825 `/scratch/stefan/7916127/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1C=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045684.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045684 none CCN1C=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 134, 134, 134, 134, 134, 105, 105, 105, 41, 26, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 134, 134, 134, 105, 41, 41, 26, 26, 4, 1] 201 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: 794 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: REAL250005045684 none CCN1C=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 44, 67, 130, 130, 130, 134, 134, 134, 134, 134, 5, 5, 5, 5, 5, 1, 1, 1, 10, 44, 44, 67, 67, 130, 134] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 489 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045684 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045684 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045684/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045684 Building REAL250005045685 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045685' /scratch/stefan/7916127/working/building/REAL250005045685 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045685 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045685/0 /scratch/stefan/7916127/working/building/REAL250005045685 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/826 `/scratch/stefan/7916127/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCCOC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045685.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045685 none O=C(CC1CCCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 157, 201, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 157, 157, 201, 201, 201, 201, 201, 201, 201, 201, 201, 44, 23, 23, 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: 744 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045685 none O=C(CC1CCCOC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 10, 1, 1, 1, 1, 1, 1, 1, 33, 33, 111, 130, 201, 201, 201, 201, 201, 201, 201, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 111, 111, 130, 130, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045685 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045685 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045685/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045685 Building REAL250005045686 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045686' /scratch/stefan/7916127/working/building/REAL250005045686 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045686 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045686/0 /scratch/stefan/7916127/working/building/REAL250005045686 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/827 `/scratch/stefan/7916127/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC=CCC1)C1=CC(=O)[N-]O1) `REAL250005045686.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045686 none O=C(NCCNC(=O)C1CCC=CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 29, 48, 124, 124, 124, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 29, 29, 48, 48, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 643 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: REAL250005045686 none O=C(NCCNC(=O)C1CCC=CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [193, 193, 104, 65, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 104, 104, 65, 65, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 724 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045686 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045686 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045686/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045686 Building REAL250005045687 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045687' /scratch/stefan/7916127/working/building/REAL250005045687 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045687 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045687/0 /scratch/stefan/7916127/working/building/REAL250005045687 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/828 `/scratch/stefan/7916127/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045687.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045687 none CC1=NC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 94, 94, 42, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 42, 42, 29, 29, 7, 1] 94 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]) 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: REAL250005045687 none CC1=NC=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 26, 44, 90, 90, 90, 94, 94, 94, 94, 94, 1, 2, 2, 2, 1, 1, 5, 26, 26, 44, 44, 90, 94] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 332 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045687 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045687 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045687/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045687 Building REAL250005045688 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045688' /scratch/stefan/7916127/working/building/REAL250005045688 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045688 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045688/0 /scratch/stefan/7916127/working/building/REAL250005045688 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/829 `/scratch/stefan/7916127/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(F)CCCC1)C1=CC(=O)[N-]O1) `REAL250005045688.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045688 none O=C(NCCNC(=O)C1(F)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 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: [11, 1, 11, 11, 30, 37, 94, 94, 94, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 11, 30, 30, 37, 37, 94, 144, 144, 144, 144, 144, 144, 144, 144, 1] 144 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 468 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: REAL250005045688 none O=C(NCCNC(=O)C1(F)CCCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 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: [135, 135, 76, 55, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 135, 144, 144, 144, 144, 144, 135, 76, 76, 55, 55, 10, 1, 1, 1, 1, 1, 1, 1, 1, 144] 144 rigid atoms, others: [32, 33, 6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 34, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 520 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045688 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045688 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045688/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045688 Building REAL250005045689 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045689' /scratch/stefan/7916127/working/building/REAL250005045689 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045689 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045689/0 /scratch/stefan/7916127/working/building/REAL250005045689 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/830 `/scratch/stefan/7916127/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045689.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045689 none CN1C=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [133, 133, 133, 133, 133, 114, 114, 115, 58, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 115, 58, 58, 35, 35, 11, 1] 133 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]) total number of confs: 437 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: REAL250005045689 none CN1C=NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 46, 73, 123, 123, 123, 133, 133, 133, 133, 133, 2, 2, 2, 1, 1, 12, 46, 46, 73, 73, 123, 133] 133 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 484 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045689 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045689 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045689/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045689 Building REAL250005045690 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045690' /scratch/stefan/7916127/working/building/REAL250005045690 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045690 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045690/0 /scratch/stefan/7916127/working/building/REAL250005045690 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/831 `/scratch/stefan/7916127/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NO1) `REAL250005045690.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045690 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.2', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 187, 187, 85, 85, 85, 35, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 187, 187, 187, 201, 201, 201, 201, 201, 85, 35, 35, 20, 20, 4, 1, 187] 201 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]) total number of confs: 518 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045690 none CCC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=NO1 NO_LONG_NAME dock atom types: ['C.3', '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.2', 'N.2', 'O.3', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens 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, 10, 10, 10, 56, 82, 174, 177, 174, 187, 187, 187, 187, 187, 1, 1, 1, 6, 6, 6, 5, 5, 10, 56, 56, 82, 82, 177, 187, 1] 201 rigid atoms, others: [1, 2, 3, 4, 33, 18, 19, 20] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 657 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045690 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045690 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045690/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045690 Building REAL250005045691 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045691' /scratch/stefan/7916127/working/building/REAL250005045691 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045691 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045691/0 /scratch/stefan/7916127/working/building/REAL250005045691 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/832 `/scratch/stefan/7916127/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045691.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045691 none O=C(CC1=CSC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 159, 201, 201, 201, 201, 29, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 159, 159, 201, 201, 69, 29, 29, 18, 18, 4, 1] 201 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]) total number of confs: 692 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045691 none O=C(CC1=CSC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 29, 29, 111, 141, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 29, 111, 111, 141, 141, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 784 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045691 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045691 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045691/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045691 Building REAL250005045692 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045692' /scratch/stefan/7916127/working/building/REAL250005045692 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045692 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045692/0 /scratch/stefan/7916127/working/building/REAL250005045692 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/833 `/scratch/stefan/7916127/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045692.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045692 none CN(C)C(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 67, 81, 40, 40, 40, 20, 15, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 67, 67, 40, 20, 20, 15, 15, 4, 1] 81 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: 329 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045692 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045692 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045692/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045692 Building REAL250005045693 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045693' /scratch/stefan/7916127/working/building/REAL250005045693 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045693 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045693/0 /scratch/stefan/7916127/working/building/REAL250005045693 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/834 `/scratch/stefan/7916127/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045693.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045693 none O=C(CCC1=CNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 169, 194, 201, 201, 201, 201, 31, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 170, 170, 195, 195, 201, 201, 201, 74, 31, 31, 21, 21, 6, 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: 813 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045693 none O=C(CCC1=CNN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 16, 8, 1, 1, 1, 1, 1, 1, 51, 51, 122, 147, 197, 197, 197, 201, 201, 201, 201, 201, 16, 16, 8, 8, 1, 1, 1, 51, 125, 125, 146, 146, 197, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 796 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045693 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045693 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045693/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045693 Building REAL250005045694 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045694' /scratch/stefan/7916127/working/building/REAL250005045694 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045694 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045694/0 /scratch/stefan/7916127/working/building/REAL250005045694 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/835 `/scratch/stefan/7916127/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CC1)C1=CC(=O)[N-]O1) `REAL250005045694.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045694 none O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 131, 45, 45, 5, 45, 5, 5, 5, 1, 5, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 146, 146, 131, 131, 45, 5, 5, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 11, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045694 none O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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] 0 hydrogens 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, 14, 23, 59, 59, 59, 165, 165, 165, 165, 165, 201, 201, 1, 1, 1, 1, 1, 1, 3, 13, 13, 23, 23, 59, 165, 165, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 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, 33, 34]) total number of confs: 629 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045694 none O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 159, 78, 63, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 159, 165, 165, 165, 165, 165, 164, 78, 78, 63, 63, 11, 1, 1, 5, 5, 5, 5, 5, 165] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35]) total number of confs: 591 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045694 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045694 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045694/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045694 Building REAL250005045695 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045695' /scratch/stefan/7916127/working/building/REAL250005045695 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045695 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045695/0 /scratch/stefan/7916127/working/building/REAL250005045695 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/836 `/scratch/stefan/7916127/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CCC1)C1=CC(=O)[N-]O1) `REAL250005045695.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045695 none O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [201, 201, 136, 106, 33, 33, 6, 33, 6, 6, 6, 1, 6, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 136, 136, 106, 106, 33, 6, 6, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045695 none O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [3, 1, 3, 3, 24, 37, 85, 85, 85, 189, 189, 189, 189, 189, 201, 201, 201, 1, 1, 1, 1, 1, 1, 3, 23, 23, 37, 37, 85, 189, 189, 201, 201, 201, 201, 201, 201, 201, 1] 201 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: 611 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045695 none O=C(NCCNC(=O)[C@@H]1C[C@H]1C1CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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: [189, 188, 92, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 6, 6, 6, 188, 189, 189, 189, 189, 189, 189, 92, 92, 61, 61, 12, 1, 1, 6, 6, 6, 6, 6, 6, 6, 189] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 691 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045695 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045695 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045695/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045695 Building REAL250005045696 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045696' /scratch/stefan/7916127/working/building/REAL250005045696 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045696 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045696/0 /scratch/stefan/7916127/working/building/REAL250005045696 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/837 `/scratch/stefan/7916127/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045696.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045696 none COCCC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 143, 103, 31, 103, 31, 31, 19, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 160, 160, 160, 160, 160, 143, 143, 103, 103, 103, 103, 31, 19, 19, 12, 12, 4, 1] 160 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: 731 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045696 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045696 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045696/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045696 Building REAL250005045697 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045697' /scratch/stefan/7916127/working/building/REAL250005045697 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045697 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045697/0 /scratch/stefan/7916127/working/building/REAL250005045697 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/838 `/scratch/stefan/7916127/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045697.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045697 none CCC(C)(CC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 161, 88, 159, 161, 167, 88, 88, 37, 22, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 161, 161, 159, 186, 186, 186, 186, 186, 88, 37, 37, 22, 22, 5, 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: 1180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045697 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045697 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045697/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045697 Building REAL250005045698 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045698' /scratch/stefan/7916127/working/building/REAL250005045698 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045698 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045698/0 /scratch/stefan/7916127/working/building/REAL250005045698 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/839 `/scratch/stefan/7916127/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045698.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045698 none COCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens need 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, 175, 91, 91, 91, 34, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 175, 175, 201, 201, 201, 200, 200, 91, 34, 34, 21, 21, 4, 1, 175, 175, 175, 175] 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: 682 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045698 none COCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 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] 0 hydrogens 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, 9, 1, 1, 1, 7, 7, 7, 47, 70, 162, 162, 162, 175, 175, 175, 175, 175, 1, 1, 26, 26, 26, 9, 9, 7, 47, 47, 70, 70, 162, 175, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 18, 19] set([0, 1, 5, 6, 7, 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: 623 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045698 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045698 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045698/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045698 Building REAL250005045699 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045699' /scratch/stefan/7916127/working/building/REAL250005045699 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045699 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045699/0 /scratch/stefan/7916127/working/building/REAL250005045699 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/840 `/scratch/stefan/7916127/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045699.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045699 none COCC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 167, 102, 167, 167, 102, 102, 38, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 167, 167, 167, 167, 167, 167, 102, 38, 38, 22, 22, 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: 860 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045699 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045699 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045699/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045699 Building REAL250005045700 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045700' /scratch/stefan/7916127/working/building/REAL250005045700 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045700 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045700/0 /scratch/stefan/7916127/working/building/REAL250005045700 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/841 `/scratch/stefan/7916127/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045700.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045700 none O=C(CCC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 131, 157, 201, 201, 201, 201, 17, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 131, 131, 157, 157, 201, 201, 49, 17, 17, 8, 8, 2, 1] 201 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]) total number of confs: 730 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045700 none O=C(CCC1=NOC=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 8, 4, 1, 1, 1, 1, 1, 1, 38, 38, 114, 139, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 4, 4, 1, 1, 38, 119, 119, 137, 137, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 786 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045700 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045700 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045700/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045700 Building REAL250005045701 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045701' /scratch/stefan/7916127/working/building/REAL250005045701 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045701 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045701/0 /scratch/stefan/7916127/working/building/REAL250005045701 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/842 `/scratch/stefan/7916127/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045701.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045701 none CC1=CN=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 141, 56, 56, 56, 24, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 141, 141, 56, 24, 24, 17, 17, 4, 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: 660 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: REAL250005045701 none CC1=CN=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 41, 41, 41, 106, 122, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 8, 8, 41, 106, 106, 122, 122, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([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]) total number of confs: 717 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045701 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045701/1 /scratch/stefan/7916127/working/building/REAL250005045701 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/843 `/scratch/stefan/7916127/working/3D/843' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C[NH+]=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045701.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045701 none CC1=C[NH+]=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 12, 12, 4, 1] 17 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: 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: REAL250005045701 none CC1=C[NH+]=CN1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 5, 5, 11, 13, 13, 13, 13, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 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/7916127/working/building/REAL250005045701 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045701 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045701/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045701/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045701 Building REAL250005045702 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045702' /scratch/stefan/7916127/working/building/REAL250005045702 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045702 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045702/0 /scratch/stefan/7916127/working/building/REAL250005045702 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/844 `/scratch/stefan/7916127/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C) `REAL250005045702.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045702 none C[C@@H]1[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', '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', 'N.4', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 14, 15, 14, 14, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 14, 8, 8, 8, 8, 6, 1, 15, 15, 15, 15, 15, 15, 15] 15 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, 39, 40]) total number of confs: 52 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: REAL250005045702 none C[C@@H]1[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', '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', 'N.4', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 8, 9, 9, 9, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 2, 2, 2, 3, 7, 7, 8, 8, 9, 15, 1, 1, 1, 1, 2, 2, 2] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 36, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 58 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045702 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045702/1 /scratch/stefan/7916127/working/building/REAL250005045702 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/845 `/scratch/stefan/7916127/working/3D/845' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C) `REAL250005045702.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045702 none C[C@@H]1[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', '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', 'N.4', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 4, 1, 14, 14, 14, 14, 14, 14, 14] 14 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, 39, 40]) total number of confs: 45 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: REAL250005045702 none C[C@@H]1[C@H](C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'H', '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', 'N.4', '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, 7, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 10, 11, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 2, 2, 2, 3, 7, 7, 10, 10, 11, 14, 1, 1, 1, 1, 2, 2, 2] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 35, 34, 19, 20, 21, 22, 23, 36, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045702 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045702 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045702/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045702/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045702 Building REAL250005045703 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045703' /scratch/stefan/7916127/working/building/REAL250005045703 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045703 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045703/0 /scratch/stefan/7916127/working/building/REAL250005045703 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/846 `/scratch/stefan/7916127/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1CCCO1)C1=CC(=O)[N-]O1) `REAL250005045703.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045703 none O=C(NCCNC(=O)[C@H]1CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 22, 30, 69, 69, 69, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 7, 22, 22, 30, 30, 69, 118, 118, 118, 118, 118, 118, 1] 118 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 377 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: REAL250005045703 none O=C(NCCNC(=O)[C@H]1CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 83, 61, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 116, 118, 118, 118, 118, 118, 116, 83, 83, 61, 61, 12, 1, 1, 1, 1, 1, 1, 118] 118 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 459 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045703 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045703 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045703/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045703 Building REAL250005045704 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045704' /scratch/stefan/7916127/working/building/REAL250005045704 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045704 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045704/0 /scratch/stefan/7916127/working/building/REAL250005045704 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/847 `/scratch/stefan/7916127/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045704.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045704 none O=C(CCC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 136, 162, 201, 201, 20, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 136, 136, 182, 182, 187, 43, 20, 20, 12, 12, 4, 1] 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]) total number of confs: 945 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045704 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045704 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045704/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045704 Building REAL250005045705 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045705' /scratch/stefan/7916127/working/building/REAL250005045705 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045705 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045705/0 /scratch/stefan/7916127/working/building/REAL250005045705 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/848 `/scratch/stefan/7916127/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045705.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045705 none COCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 199, 127, 127, 127, 42, 26, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 199, 199, 199, 201, 201, 201, 201, 201, 127, 42, 42, 26, 26, 7, 1, 199, 199, 199, 199, 199, 199] 201 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: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045705 none COCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 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, 3, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 1, 1, 1, 6, 6, 6, 39, 70, 188, 193, 193, 199, 199, 199, 199, 199, 1, 1, 1, 14, 14, 14, 6, 6, 6, 39, 39, 70, 70, 193, 199, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [33, 2, 3, 4, 37, 35, 34, 18, 19, 20, 36, 38] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045705 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045705 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045705/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045705 Building REAL250005045706 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045706' /scratch/stefan/7916127/working/building/REAL250005045706 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045706 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045706/0 /scratch/stefan/7916127/working/building/REAL250005045706 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/849 `/scratch/stefan/7916127/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(F)F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045706.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045706 none CC(CC(F)F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 59, 136, 185, 201, 201, 59, 59, 23, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 136, 136, 136, 136, 185, 185, 201, 59, 23, 23, 14, 14, 4, 1] 201 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]) total number of confs: 923 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045706 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045706 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045706/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045706 Building REAL250005045707 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045707' /scratch/stefan/7916127/working/building/REAL250005045707 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045707 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045707/0 /scratch/stefan/7916127/working/building/REAL250005045707 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/850 `/scratch/stefan/7916127/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(F)=CN1) `REAL250005045707.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045707 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(F)=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [8, 1, 8, 8, 38, 60, 109, 109, 109, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 8, 38, 38, 60, 60, 109, 117, 1, 1, 1] 117 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 417 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045707 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC(F)=CN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'F', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 15, 1, 8, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 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: [87, 87, 42, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 87, 117, 117, 117, 117, 117, 87, 42, 42, 26, 26, 9, 1, 117, 117, 117] 117 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]) total number of confs: 353 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045707 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045707 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045707/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045707 Building REAL250005045708 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045708' /scratch/stefan/7916127/working/building/REAL250005045708 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045708 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045708/0 /scratch/stefan/7916127/working/building/REAL250005045708 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/851 `/scratch/stefan/7916127/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045708.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045708 none CC1(CC(=O)NCCNC(=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', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 182, 75, 75, 75, 32, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 185, 185, 75, 32, 32, 21, 21, 4, 1, 201, 201, 201, 201] 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: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045708 none CC1(CC(=O)NCCNC(=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', '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, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens 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, 7, 29, 29, 29, 106, 129, 200, 201, 200, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 7, 7, 29, 106, 106, 129, 129, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 32, 34, 17, 18, 31] set([3, 4, 5, 6, 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: 768 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045708 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045708 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045708/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045708 Building REAL250005045709 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045709' /scratch/stefan/7916127/working/building/REAL250005045709 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045709 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045709/0 /scratch/stefan/7916127/working/building/REAL250005045709 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/852 `/scratch/stefan/7916127/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CNC(=O)C1) `REAL250005045709.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045709 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CNC(=O)C1 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', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 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: [172, 110, 110, 110, 48, 31, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 172, 172, 172, 172, 172, 172, 172, 172, 110, 48, 48, 31, 31, 10, 1, 172, 172, 172, 172, 172] 172 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 582 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: REAL250005045709 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CNC(=O)C1 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', 'N.am', 'C.2', 'O.2', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 6, 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: [1, 1, 1, 6, 6, 6, 36, 66, 164, 164, 164, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 2, 2, 2, 6, 36, 36, 66, 66, 164, 172, 1, 1, 1, 1, 1] 172 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 591 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045709 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045709 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045709/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045709 Building REAL250005045710 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045710' /scratch/stefan/7916127/working/building/REAL250005045710 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045710 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045710/0 /scratch/stefan/7916127/working/building/REAL250005045710 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/853 `/scratch/stefan/7916127/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC2CC2C1) `REAL250005045710.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045710 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC2CC2C1 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', '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, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 117, 117, 117, 52, 31, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 117, 52, 52, 31, 31, 7, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 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: 685 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: REAL250005045710 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC2CC2C1 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', '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, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 48, 81, 194, 194, 194, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 2, 2, 2, 7, 48, 48, 81, 81, 194, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 36, 33, 38, 32, 34, 16, 17, 18, 19, 20, 37, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 691 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045710 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045710 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045710/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045710 Building REAL250005045711 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045711' /scratch/stefan/7916127/working/building/REAL250005045711 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045711 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045711/0 /scratch/stefan/7916127/working/building/REAL250005045711 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/854 `/scratch/stefan/7916127/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CCF)CC1)C1=CC(=O)[N-]O1) `REAL250005045711.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045711 none O=C(NCCNC(=O)C1(CCF)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens 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, 3, 18, 26, 72, 72, 72, 136, 201, 201, 136, 136, 1, 1, 1, 1, 1, 1, 4, 18, 18, 26, 26, 72, 201, 201, 201, 201, 136, 136, 136, 136, 1] 201 rigid atoms, others: [1, 34, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 779 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: REAL250005045711 none O=C(NCCNC(=O)C1(CCF)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 53, 38, 7, 7, 1, 7, 1, 1, 7, 18, 1, 1, 128, 136, 136, 136, 136, 136, 128, 53, 53, 38, 38, 7, 7, 7, 18, 18, 1, 1, 1, 1, 136] 201 rigid atoms, others: [32, 33, 6, 8, 9, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34]) total number of confs: 504 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045711 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045711 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045711/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045711 Building REAL250005045712 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045712' /scratch/stefan/7916127/working/building/REAL250005045712 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045712 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045712/0 /scratch/stefan/7916127/working/building/REAL250005045712 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/855 `/scratch/stefan/7916127/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045712.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045712 none COCC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [119, 119, 87, 42, 87, 87, 19, 19, 19, 17, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 119, 119, 119, 119, 119, 87, 87, 87, 87, 87, 87, 42, 42, 19, 17, 17, 10, 10, 2, 1] 119 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: 554 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045712 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045712 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045712/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045712 Building REAL250005045713 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045713' /scratch/stefan/7916127/working/building/REAL250005045713 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045713 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045713/0 /scratch/stefan/7916127/working/building/REAL250005045713 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/856 `/scratch/stefan/7916127/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COCC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045713.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045713 none O=C(COCC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 79, 135, 189, 201, 201, 13, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 79, 79, 189, 189, 201, 35, 13, 13, 10, 10, 2, 1] 201 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]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045713 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045713 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045713/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045713 Building REAL250005045714 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045714' /scratch/stefan/7916127/working/building/REAL250005045714 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045714 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045714/0 /scratch/stefan/7916127/working/building/REAL250005045714 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/857 `/scratch/stefan/7916127/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@]12C[C@H]1COC2)C1=CC(=O)[N-]O1) `REAL250005045714.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045714 none O=C(NCCNC(=O)[C@]12C[C@H]1COC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 33, 50, 108, 108, 108, 199, 199, 199, 199, 199, 199, 1, 1, 1, 1, 1, 1, 7, 32, 32, 50, 50, 108, 199, 199, 199, 199, 199, 199, 1] 199 rigid atoms, others: [1, 33, 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]) total number of confs: 514 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: REAL250005045714 none O=C(NCCNC(=O)[C@]12C[C@H]1COC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [188, 187, 89, 47, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 187, 199, 199, 199, 199, 199, 188, 89, 89, 47, 47, 6, 1, 1, 1, 1, 1, 1, 199] 199 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 33, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 703 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045714 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045714 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045714/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045714 Building REAL250005045715 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045715' /scratch/stefan/7916127/working/building/REAL250005045715 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types Protomer extracton resulted in 0 protomers Marking REAL250005045715 as failed and skipping /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `/scratch/stefan/7916127/failed' `/scratch/stefan/7916127/working/building/REAL250005045715' -> `/scratch/stefan/7916127/failed/REAL250005045715' Building REAL250005045716 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045716' /scratch/stefan/7916127/working/building/REAL250005045716 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045716 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045716/0 /scratch/stefan/7916127/working/building/REAL250005045716 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/858 `/scratch/stefan/7916127/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045716.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045716 none CC1(C(=O)NCCNC(=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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 92, 92, 92, 48, 29, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 92, 48, 48, 29, 29, 7, 1, 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]) total number of confs: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045716 none CC1(C(=O)NCCNC(=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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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] 0 hydrogens 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, 7, 7, 7, 49, 98, 191, 191, 191, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 7, 49, 49, 98, 98, 191, 201, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 16, 17, 28, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 744 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045716 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045716 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045716/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045716 Building REAL250005045717 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045717' /scratch/stefan/7916127/working/building/REAL250005045717 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045717 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045717/0 /scratch/stefan/7916127/working/building/REAL250005045717 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/859 `/scratch/stefan/7916127/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNC=C1) `REAL250005045717.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045717 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 33, 65, 123, 123, 123, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 5, 33, 33, 65, 65, 123, 133, 1, 1, 1, 1] 133 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 467 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045717 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CNC=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 1, 1, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 48, 29, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 95, 133, 133, 133, 133, 95, 48, 48, 29, 29, 9, 1, 133, 133, 133, 133] 133 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045717 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045717 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045717/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045717 Building REAL250005045718 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045718' /scratch/stefan/7916127/working/building/REAL250005045718 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045718 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045718/0 /scratch/stefan/7916127/working/building/REAL250005045718 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/860 `/scratch/stefan/7916127/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCCC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045718.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045718 none CC1CCCC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 111, 111, 111, 42, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 42, 42, 24, 24, 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: 798 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: REAL250005045718 none CC1CCCC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 15, 72, 109, 198, 201, 198, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 72, 72, 109, 109, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 768 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045718 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045718 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045718/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045718 Building REAL250005045719 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045719' /scratch/stefan/7916127/working/building/REAL250005045719 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045719 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045719/0 /scratch/stefan/7916127/working/building/REAL250005045719 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/861 `/scratch/stefan/7916127/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)NC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045719.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045719 none CCC(=O)NC(C)C(=O)NCCNC(=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.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', '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, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 149, 149, 149, 132, 69, 132, 69, 69, 31, 21, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 149, 132, 132, 132, 132, 69, 31, 31, 21, 21, 9, 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: 890 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045719 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045719 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045719/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045719 Building REAL250005045720 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045720' /scratch/stefan/7916127/working/building/REAL250005045720 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045720 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045720/0 /scratch/stefan/7916127/working/building/REAL250005045720 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/862 `/scratch/stefan/7916127/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1=O) `REAL250005045720.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045720 none CN1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 114, 114, 114, 45, 33, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 114, 45, 45, 33, 33, 9, 1, 201, 201] 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]) total number of confs: 640 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: REAL250005045720 none CN1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 57, 94, 187, 189, 187, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 57, 57, 94, 94, 189, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 35, 34, 18, 19, 20, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 731 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045720 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045720 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045720/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045720 Building REAL250005045721 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045721' /scratch/stefan/7916127/working/building/REAL250005045721 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045721 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045721/0 /scratch/stefan/7916127/working/building/REAL250005045721 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/863 `/scratch/stefan/7916127/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045721.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045721 none CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', 'H', '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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 13, 35, 35, 35, 97, 114, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 3, 3, 3, 2, 13, 13, 35, 97, 97, 114, 114, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 33, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 733 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: REAL250005045721 none CC(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', 'H', '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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 165, 67, 67, 67, 32, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 199, 166, 166, 67, 32, 32, 22, 22, 4, 1, 201, 201, 201, 201, 201] 201 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]) total number of confs: 827 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045721 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045721 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045721/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045721 Building REAL250005045722 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045722' /scratch/stefan/7916127/working/building/REAL250005045722 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045722 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045722/0 /scratch/stefan/7916127/working/building/REAL250005045722 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/864 `/scratch/stefan/7916127/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(C2CC2)CCC1)C1=CC(=O)[N-]O1) `REAL250005045722.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045722 none O=C(NCCNC(=O)C1(C2CC2)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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, 108, 77, 17, 17, 8, 17, 1, 1, 1, 1, 8, 8, 8, 201, 201, 201, 201, 201, 201, 201, 108, 108, 77, 77, 17, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 201] 201 rigid atoms, others: [8, 9, 10, 11, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 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: 727 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045722 none O=C(NCCNC(=O)C1(C2CC2)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [5, 1, 5, 5, 23, 38, 97, 97, 97, 157, 201, 201, 157, 157, 157, 1, 1, 1, 1, 1, 1, 5, 23, 23, 38, 38, 97, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 157, 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: 698 number of broken/clashed sets: 49 ./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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045722 none O=C(NCCNC(=O)C1(C2CC2)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [151, 150, 53, 32, 6, 6, 1, 6, 1, 1, 8, 8, 1, 1, 1, 150, 157, 157, 157, 157, 157, 151, 53, 53, 32, 32, 6, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 157] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 7, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 517 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045722 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045722 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045722/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045722 Building REAL250005045723 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045723' /scratch/stefan/7916127/working/building/REAL250005045723 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045723 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045723/0 /scratch/stefan/7916127/working/building/REAL250005045723 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/865 `/scratch/stefan/7916127/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1) `REAL250005045723.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045723 none COC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [153, 137, 137, 137, 109, 109, 109, 43, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 137, 137, 153, 153, 153, 109, 43, 43, 28, 28, 7, 1, 137] 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]) 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: REAL250005045723 none COC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 8, 8, 8, 34, 55, 131, 131, 131, 137, 137, 137, 137, 137, 1, 1, 7, 7, 7, 8, 34, 34, 56, 56, 131, 137, 1] 153 rigid atoms, others: [1, 2, 3, 4, 5, 19, 20, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 464 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045723 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045723 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045723/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045723 Building REAL250005045724 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045724' /scratch/stefan/7916127/working/building/REAL250005045724 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045724 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045724/0 /scratch/stefan/7916127/working/building/REAL250005045724 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/866 `/scratch/stefan/7916127/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005045724.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045724 none CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 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, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 17, 17, 17, 77, 98, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 17, 77, 77, 98, 98, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 720 number of broken/clashed sets: 150 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045724 none CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 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, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 60, 150, 60, 60, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 151, 151, 150, 151, 150, 151, 60, 21, 21, 14, 14, 4, 1, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 804 number of broken/clashed sets: 150 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045724 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045724 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045724/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045724 Building REAL250005045725 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045725' /scratch/stefan/7916127/working/building/REAL250005045725 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045725 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045725/0 /scratch/stefan/7916127/working/building/REAL250005045725 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/867 `/scratch/stefan/7916127/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005045725.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045725 none COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 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, 6, 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, 4, 7, 6, 7, 7, 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: [13, 9, 1, 9, 24, 24, 24, 86, 115, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 13, 13, 13, 9, 24, 86, 86, 115, 115, 201, 201, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 35, 36, 37, 38, 34, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 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: REAL250005045725 none COC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 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, 6, 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, 4, 7, 6, 7, 7, 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: [162, 152, 103, 103, 103, 32, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 162, 162, 162, 152, 103, 32, 32, 20, 20, 4, 1, 201, 201, 201, 201, 201, 201, 201] 201 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, 38]) total number of confs: 779 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045725 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045725 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045725/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045725 Building REAL250005045726 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045726' /scratch/stefan/7916127/working/building/REAL250005045726 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045726 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045726/0 /scratch/stefan/7916127/working/building/REAL250005045726 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/868 `/scratch/stefan/7916127/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSN=N1) `REAL250005045726.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045726 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [7, 1, 7, 7, 27, 40, 75, 75, 75, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 7, 27, 27, 40, 40, 75, 81, 1] 81 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045726 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSN=N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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: [75, 75, 43, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 75, 81, 81, 81, 81, 75, 43, 43, 32, 32, 11, 1, 81] 81 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26]) total number of confs: 266 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045726 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045726 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045726/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045726 Building REAL250005045727 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045727' /scratch/stefan/7916127/working/building/REAL250005045727 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045727 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045727/0 /scratch/stefan/7916127/working/building/REAL250005045727 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/869 `/scratch/stefan/7916127/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005045727.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045727 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 102, 102, 102, 52, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 186, 186, 102, 52, 52, 34, 34, 10, 1, 186, 186, 186, 186, 186, 186, 186, 186] 186 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: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045727 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 5, 5, 5, 36, 71, 175, 175, 175, 186, 186, 186, 186, 186, 1, 1, 1, 1, 2, 2, 2, 5, 36, 36, 71, 71, 175, 186, 1, 1, 1, 1, 1, 1, 1, 1] 186 rigid atoms, others: [0, 1, 2, 35, 36, 33, 32, 34, 16, 17, 18, 19, 37, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045727 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045727 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045727/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045727 Building REAL250005045728 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045728' /scratch/stefan/7916127/working/building/REAL250005045728 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045728 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045728/0 /scratch/stefan/7916127/working/building/REAL250005045728 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/870 `/scratch/stefan/7916127/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CN=CO1) `REAL250005045728.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045728 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CN=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 21, 36, 72, 72, 72, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 7, 21, 21, 36, 36, 72, 80, 1, 1] 80 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 284 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045728 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CN=CO1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 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: [68, 68, 38, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 68, 80, 80, 80, 80, 68, 38, 38, 23, 23, 7, 1, 80, 80] 80 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 275 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045728 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045728 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045728/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045728 Building REAL250005045729 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045729' /scratch/stefan/7916127/working/building/REAL250005045729 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045729 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045729/0 /scratch/stefan/7916127/working/building/REAL250005045729 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/871 `/scratch/stefan/7916127/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCN1C=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045729.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045729 none O=C(CCN1C=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 120, 134, 201, 201, 201, 201, 20, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 120, 120, 134, 134, 201, 201, 201, 52, 20, 20, 11, 11, 4, 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: 668 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045729 none O=C(CCN1C=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 15, 8, 1, 1, 1, 1, 1, 1, 56, 56, 138, 160, 201, 201, 201, 201, 201, 201, 201, 201, 15, 15, 8, 8, 1, 1, 1, 56, 142, 142, 159, 159, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 807 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045729 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045729 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045729/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045729 Building REAL250005045730 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045730' /scratch/stefan/7916127/working/building/REAL250005045730 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045730 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045730/0 /scratch/stefan/7916127/working/building/REAL250005045730 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/872 `/scratch/stefan/7916127/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045730.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045730 none CNC(=O)NCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 4, 7, 6, 4, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 178, 178, 178, 139, 86, 86, 86, 32, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 178, 139, 139, 86, 32, 32, 20, 20, 4, 1] 201 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]) total number of confs: 783 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045730 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045730 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045730/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045730 Building REAL250005045731 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045731' /scratch/stefan/7916127/working/building/REAL250005045731 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045731 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045731/0 /scratch/stefan/7916127/working/building/REAL250005045731 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/873 `/scratch/stefan/7916127/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045731.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045731 none O=C(CCC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [39, 39, 39, 84, 99, 123, 123, 123, 123, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 85, 85, 99, 99, 123, 123, 123, 39, 21, 21, 14, 14, 4, 1] 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]) total number of confs: 461 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045731 none O=C(CCC1=CNC=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 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] 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: [41, 14, 6, 1, 1, 1, 1, 1, 1, 41, 41, 85, 103, 123, 123, 123, 123, 123, 123, 123, 123, 14, 14, 6, 6, 1, 1, 1, 41, 85, 85, 103, 103, 123, 123] 123 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 522 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045731 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045731/1 /scratch/stefan/7916127/working/building/REAL250005045731 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/874 `/scratch/stefan/7916127/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCC1=CN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045731.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045731 none O=C(CCC1=CN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 149, 179, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 150, 150, 180, 180, 201, 201, 201, 58, 23, 23, 14, 14, 4, 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: 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: REAL250005045731 none O=C(CCC1=CN=CN1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'N.am', '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: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 9, 5, 1, 1, 1, 1, 1, 1, 41, 41, 118, 146, 200, 201, 200, 201, 201, 201, 201, 201, 9, 9, 5, 5, 1, 1, 1, 41, 122, 122, 145, 145, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 25, 26, 27] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 805 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045731 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045731 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045731/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045731/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045731 Building REAL250005045732 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045732' /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045732 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045732/0 /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/875 `/scratch/stefan/7916127/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005045732.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045732 none C[N@H+](CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 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, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 13, 13, 13, 20, 20, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 3, 3, 7, 7, 13, 20, 20, 20, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 92 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: REAL250005045732 none C[N@H+](CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 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, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 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, 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, 23, 15, 15, 15, 9, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 20, 20, 15, 9, 9, 7, 7, 4, 1, 23, 23, 23, 23, 23, 23, 23] 23 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, 39, 40]) total number of confs: 95 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045732/1 /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/876 `/scratch/stefan/7916127/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005045732.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045732 none C[N@@H+](CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 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, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 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, 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: [2, 1, 2, 2, 8, 14, 14, 14, 21, 21, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 2, 2, 2, 8, 8, 14, 21, 21, 21, 21, 24, 24, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [1, 34, 35, 36, 37, 38, 39, 40, 18, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 95 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: REAL250005045732 none C[N@@H+](CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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'] dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 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, 7] dock color type numbers: [7, 1, 7, 7, 7, 6, 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, 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, 21, 24, 16, 16, 16, 10, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 21, 21, 16, 10, 10, 8, 8, 4, 1, 24, 24, 24, 24, 24, 24, 24] 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, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 98 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045732/2 /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/877 `/scratch/stefan/7916127/working/3D/877' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1) `REAL250005045732.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045732/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045732 none CN(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.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'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 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: [4, 1, 4, 9, 18, 18, 18, 52, 71, 107, 107, 107, 108, 108, 108, 108, 108, 1, 1, 1, 1, 4, 4, 4, 9, 9, 18, 52, 52, 71, 71, 107, 108, 1, 1, 1, 1, 1, 1, 1] 108 rigid atoms, others: [1, 34, 35, 36, 37, 38, 33, 39, 17, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045732 none CN(CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.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'] dock atom type numbers: [5, 10, 5, 1, 11, 8, 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, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 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, 105, 75, 75, 75, 30, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 108, 108, 108, 108, 108, 108, 108, 105, 105, 75, 30, 30, 18, 18, 5, 1, 108, 108, 108, 108, 108, 108, 108] 108 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]) total number of confs: 407 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045732 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045732 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045732/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045732/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045732/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045732 Building REAL250005045733 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045733' /scratch/stefan/7916127/working/building/REAL250005045733 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045733 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045733/0 /scratch/stefan/7916127/working/building/REAL250005045733 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/878 `/scratch/stefan/7916127/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=C(F)C=N1)C1=CC(=O)[N-]O1) `REAL250005045733.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045733 none O=C(NCCNC(=O)C1=CC=C(F)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 4, 14, 19, 37, 37, 37, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 4, 14, 14, 19, 19, 37, 63, 63, 63, 1] 63 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 166 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045733 none O=C(NCCNC(=O)C1=CC=C(F)C=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 43, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 43, 43, 34, 34, 10, 1, 1, 1, 63] 63 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 228 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045733 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045733 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045733/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045733 Building REAL250005045734 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045734' /scratch/stefan/7916127/working/building/REAL250005045734 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045734 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045734/0 /scratch/stefan/7916127/working/building/REAL250005045734 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/879 `/scratch/stefan/7916127/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045734.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045734 none C=CCCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 132, 82, 74, 34, 34, 34, 17, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 132, 132, 74, 74, 34, 17, 17, 10, 10, 2, 1] 201 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: 955 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045734 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045734 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045734/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045734 Building REAL250005045735 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045735' /scratch/stefan/7916127/working/building/REAL250005045735 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045735 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045735/0 /scratch/stefan/7916127/working/building/REAL250005045735 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/880 `/scratch/stefan/7916127/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045735.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045735 none C=CCOC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 117, 87, 50, 87, 50, 50, 22, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 87, 87, 87, 87, 50, 22, 22, 13, 13, 4, 1] 201 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: 811 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045735 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045735 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045735/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045735 Building REAL250005045736 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045736' /scratch/stefan/7916127/working/building/REAL250005045736 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045736 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045736/0 /scratch/stefan/7916127/working/building/REAL250005045736 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/881 `/scratch/stefan/7916127/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)OCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045736.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045736 none CC(C)OCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 189, 201, 121, 119, 121, 73, 73, 73, 26, 18, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 120, 120, 121, 121, 121, 121, 73, 26, 26, 18, 18, 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: 665 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045736 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045736 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045736/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045736 Building REAL250005045737 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045737' /scratch/stefan/7916127/working/building/REAL250005045737 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045737 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045737/0 /scratch/stefan/7916127/working/building/REAL250005045737 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/882 `/scratch/stefan/7916127/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045737.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045737 none NC(=O)CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 113, 113, 53, 53, 53, 29, 24, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 201, 201, 158, 158, 137, 137, 113, 113, 53, 29, 29, 24, 24, 10, 1] 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]) total number of confs: 938 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045737 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045737 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045737/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045737 Building REAL250005045738 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045738' /scratch/stefan/7916127/working/building/REAL250005045738 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045738 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045738/0 /scratch/stefan/7916127/working/building/REAL250005045738 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/883 `/scratch/stefan/7916127/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[NH+]1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045738.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045738 none C[NH+]1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 65, 65, 65, 29, 27, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 65, 29, 29, 27, 27, 11, 1, 99, 99, 99, 99] 99 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, 39, 40]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045738 none C[NH+]1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 46, 61, 71, 71, 71, 99, 99, 99, 99, 99, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 13, 46, 46, 61, 61, 71, 99, 1, 1, 1, 1] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 38, 40, 20, 21, 25, 26, 27, 28, 29, 37] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 340 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045738 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045738 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045738/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045738 Building REAL250005045739 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045739' /scratch/stefan/7916127/working/building/REAL250005045739 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045739 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045739/0 /scratch/stefan/7916127/working/building/REAL250005045739 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/884 `/scratch/stefan/7916127/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045739.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045739 none CC1=NNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 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, 111, 111, 75, 75, 75, 39, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 75, 39, 39, 28, 28, 11, 1] 111 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]) total number of confs: 308 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: REAL250005045739 none CC1=NNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 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, 10, 10, 10, 50, 65, 105, 105, 105, 111, 111, 111, 111, 111, 2, 2, 2, 1, 1, 10, 50, 50, 65, 65, 105, 111] 111 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 406 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045739 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045739 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045739/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045739 Building REAL250005045740 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045740' /scratch/stefan/7916127/working/building/REAL250005045740 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045740 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045740/0 /scratch/stefan/7916127/working/building/REAL250005045740 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/885 `/scratch/stefan/7916127/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1) `REAL250005045740.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045740 none C#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 77, 49, 32, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 49, 49, 32, 32, 11, 1, 77, 77] 77 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: 292 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045740 none C#CC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 1, 3, 3, 3, 15, 35, 67, 67, 67, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 3, 15, 15, 35, 35, 67, 77, 1, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24, 33] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045740 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045740 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045740/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045740 Building REAL250005045741 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045741' /scratch/stefan/7916127/working/building/REAL250005045741 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045741 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045741/0 /scratch/stefan/7916127/working/building/REAL250005045741 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/886 `/scratch/stefan/7916127/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NN=N1) `REAL250005045741.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045741 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NN=N1 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', 'N.pl3', 'N.2', 'N.2', '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, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 102, 102, 102, 47, 36, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 102, 47, 47, 36, 36, 13, 1, 162] 162 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]) total number of confs: 424 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: REAL250005045741 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NN=N1 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', 'N.pl3', 'N.2', 'N.2', '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, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 53, 85, 154, 154, 154, 162, 162, 162, 162, 162, 1, 1, 1, 2, 2, 2, 11, 53, 53, 85, 85, 154, 162, 1] 162 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 603 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045741 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045741/1 /scratch/stefan/7916127/working/building/REAL250005045741 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/887 `/scratch/stefan/7916127/working/3D/887' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045741.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045741 none CC1=NNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 81, 38, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 38, 38, 28, 28, 7, 1] 81 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]) total number of confs: 268 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045741 none CC1=NNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 6, 4, 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 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, 1, 3, 3, 3, 19, 36, 79, 79, 79, 81, 81, 81, 81, 81, 2, 2, 2, 1, 3, 19, 19, 36, 36, 79, 81] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045741 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045741 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045741/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045741/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045741 Building REAL250005045742 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045742' /scratch/stefan/7916127/working/building/REAL250005045742 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045742 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045742/0 /scratch/stefan/7916127/working/building/REAL250005045742 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/888 `/scratch/stefan/7916127/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045742.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045742 none CCCC(OC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 183, 112, 67, 112, 123, 67, 67, 24, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 196, 201, 188, 188, 112, 123, 123, 123, 67, 24, 24, 13, 13, 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: 944 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045742 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045742 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045742/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045742 Building REAL250005045743 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045743' /scratch/stefan/7916127/working/building/REAL250005045743 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045743 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045743/0 /scratch/stefan/7916127/working/building/REAL250005045743 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/889 `/scratch/stefan/7916127/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)C(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045743.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045743 none C=C(C)C(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need 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, 92, 196, 196, 92, 92, 35, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 197, 196, 197, 197, 197, 196, 92, 35, 35, 22, 22, 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: 792 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045743 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045743 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045743/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045743 Building REAL250005045744 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045744' /scratch/stefan/7916127/working/building/REAL250005045744 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045744 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045744/0 /scratch/stefan/7916127/working/building/REAL250005045744 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/890 `/scratch/stefan/7916127/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045744.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045744 none CC(CC(N)=O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 6, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 53, 138, 189, 201, 201, 53, 54, 25, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 138, 138, 137, 138, 189, 189, 201, 201, 54, 25, 25, 17, 17, 4, 1] 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]) total number of confs: 876 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045744 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045744 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045744/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045744 Building REAL250005045745 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045745' /scratch/stefan/7916127/working/building/REAL250005045745 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045745 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045745/0 /scratch/stefan/7916127/working/building/REAL250005045745 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/891 `/scratch/stefan/7916127/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C1CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045745.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045745 none NC(=O)C1CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 18, 18, 18, 11, 11, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 18, 11, 11, 11, 11, 8, 1] 22 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: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045745 none NC(=O)C1CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 6, 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] 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: [4, 1, 4, 1, 1, 1, 1, 1, 7, 7, 7, 17, 19, 19, 19, 19, 22, 22, 22, 22, 22, 4, 4, 1, 1, 1, 1, 1, 1, 7, 17, 17, 19, 19, 19, 22] 22 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045745 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045745 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045745/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045745 Building REAL250005045746 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045746' /scratch/stefan/7916127/working/building/REAL250005045746 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045746 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045746/0 /scratch/stefan/7916127/working/building/REAL250005045746 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/892 `/scratch/stefan/7916127/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCNC1=O)C1=CC(=O)[N-]O1) `REAL250005045746.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045746 none O=C(NCCNC(=O)C1CCNC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 34, 53, 142, 142, 142, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 34, 34, 53, 53, 142, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 654 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: REAL250005045746 none O=C(NCCNC(=O)C1CCNC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 191, 110, 76, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 191, 201, 201, 201, 201, 201, 193, 110, 110, 76, 76, 12, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 747 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045746 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045746 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045746/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045746 Building REAL250005045747 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045747' /scratch/stefan/7916127/working/building/REAL250005045747 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045747 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045747/0 /scratch/stefan/7916127/working/building/REAL250005045747 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/893 `/scratch/stefan/7916127/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045747.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045747 none CN1C(=O)NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [166, 166, 166, 166, 166, 166, 107, 107, 107, 40, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 166, 166, 166, 166, 166, 107, 40, 40, 29, 29, 10, 1] 166 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: 439 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: REAL250005045747 none CN1C(=O)NC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 6, 4, 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 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 64, 105, 161, 161, 161, 166, 166, 166, 166, 166, 2, 2, 2, 1, 1, 12, 64, 64, 105, 105, 161, 166] 166 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 641 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045747 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045747 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045747/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045747 Building REAL250005045748 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045748' /scratch/stefan/7916127/working/building/REAL250005045748 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045748 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045748/0 /scratch/stefan/7916127/working/building/REAL250005045748 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/894 `/scratch/stefan/7916127/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC1=O) `REAL250005045748.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045748 none CN1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 136, 136, 136, 57, 37, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 167, 167, 167, 167, 136, 57, 57, 37, 37, 11, 1, 167] 167 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]) total number of confs: 557 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045748 none CN1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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', 'N.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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] 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: [1, 1, 1, 1, 1, 10, 10, 10, 53, 94, 154, 155, 155, 167, 167, 167, 167, 167, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 53, 53, 94, 94, 155, 167, 1] 167 rigid atoms, others: [0, 1, 2, 3, 4, 34, 18, 19, 20, 24, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 615 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045748 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045748 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045748/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045748 Building REAL250005045749 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045749' /scratch/stefan/7916127/working/building/REAL250005045749 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045749 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045749/0 /scratch/stefan/7916127/working/building/REAL250005045749 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/895 `/scratch/stefan/7916127/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045749.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045749 none C=CC(C)(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 101, 199, 199, 101, 101, 31, 22, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 199, 201, 201, 201, 199, 101, 31, 31, 22, 22, 4, 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: 778 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045749 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045749 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045749/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045749 Building REAL250005045750 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045750' /scratch/stefan/7916127/working/building/REAL250005045750 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045750 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045750/0 /scratch/stefan/7916127/working/building/REAL250005045750 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/896 `/scratch/stefan/7916127/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045750.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045750 none C#CCCCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 114, 103, 95, 27, 27, 27, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 197, 197, 132, 132, 114, 114, 107, 107, 95, 95, 27, 27, 27, 16, 16, 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: 977 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045750 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045750 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045750/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045750 Building REAL250005045751 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045751' /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045751 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045751/0 /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/897 `/scratch/stefan/7916127/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045751.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045751 none C[N@@H+]1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 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, 8, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 6, 1] 9 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: 26 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: REAL250005045751 none C[N@@H+]1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 6, 6, 6, 6, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 5, 5, 6, 6, 6, 9] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 37 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045751/1 /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/898 `/scratch/stefan/7916127/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045751.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045751 none C[N@H+]1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 8, 1] 23 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: 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: REAL250005045751 none C[N@H+]1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 15, 16, 16, 16, 23, 23, 23, 23, 23, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 11, 11, 15, 15, 16, 23] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045751/2 /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/899 `/scratch/stefan/7916127/working/3D/899' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045751.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045751/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045751 none CN1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 85, 94, 85, 85, 38, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 94, 85, 38, 38, 27, 27, 8, 1] 94 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: 303 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045751 none CN1CCC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 52, 91, 91, 91, 94, 94, 94, 94, 94, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 34, 34, 52, 52, 91, 94] 94 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 24, 25, 26, 27, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045751 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045751 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045751/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045751/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045751/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045751 Building REAL250005045752 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045752' /scratch/stefan/7916127/working/building/REAL250005045752 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045752 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045752/0 /scratch/stefan/7916127/working/building/REAL250005045752 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/900 `/scratch/stefan/7916127/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045752.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045752 none C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 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', 'N.am', 'C.2', 'O.2', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 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, 102, 201, 102, 102, 48, 29, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 102, 48, 48, 29, 29, 6, 1] 201 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]) total number of confs: 659 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045752 none C[C@@H]1C[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 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', 'N.am', 'C.2', 'O.2', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 66, 111, 189, 189, 189, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 66, 66, 111, 111, 189, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 749 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045752 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045752 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045752/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045752 Building REAL250005045753 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045753' /scratch/stefan/7916127/working/building/REAL250005045753 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045753 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045753/0 /scratch/stefan/7916127/working/building/REAL250005045753 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/901 `/scratch/stefan/7916127/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CC=CCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045753.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045753 none O=C(CC1CC=CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 1, 1, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 156, 201, 201, 201, 201, 201, 24, 17, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 156, 156, 201, 201, 201, 201, 201, 201, 201, 201, 201, 44, 24, 24, 17, 17, 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: 747 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045753 none O=C(CC1CC=CCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 1, 1, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 32, 32, 111, 135, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 111, 111, 135, 135, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 726 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045753 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045753 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045753/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045753 Building REAL250005045754 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045754' /scratch/stefan/7916127/working/building/REAL250005045754 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045754 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045754/0 /scratch/stefan/7916127/working/building/REAL250005045754 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/902 `/scratch/stefan/7916127/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045754.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045754 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 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', '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, 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, 4, 7, 6, 7, 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: [201, 79, 79, 79, 40, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 79, 40, 40, 28, 28, 7, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34]) total number of confs: 620 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045754 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 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', '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, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 48, 98, 193, 193, 193, 201, 201, 201, 201, 201, 1, 1, 1, 2, 2, 2, 7, 48, 48, 98, 98, 193, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 33, 32, 34, 16, 17, 18, 29, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 764 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045754 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045754 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045754/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045754 Building REAL250005045755 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045755' /scratch/stefan/7916127/working/building/REAL250005045755 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045755 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045755/0 /scratch/stefan/7916127/working/building/REAL250005045755 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/903 `/scratch/stefan/7916127/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045755.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045755 none CCC(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 183, 108, 184, 108, 108, 35, 22, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 200, 184, 108, 35, 35, 22, 22, 5, 1] 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]) total number of confs: 804 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045755 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045755 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045755/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045755 Building REAL250005045756 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045756' /scratch/stefan/7916127/working/building/REAL250005045756 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045756 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045756/0 /scratch/stefan/7916127/working/building/REAL250005045756 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/904 `/scratch/stefan/7916127/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCF)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045756.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045756 none O=C(CCCF)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 159, 181, 201, 21, 14, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 159, 159, 186, 186, 201, 201, 51, 21, 21, 14, 14, 4, 1] 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]) total number of confs: 905 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045756 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045756 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045756/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045756 Building REAL250005045757 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045757' /scratch/stefan/7916127/working/building/REAL250005045757 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045757 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045757/0 /scratch/stefan/7916127/working/building/REAL250005045757 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/905 `/scratch/stefan/7916127/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(F)(F)F) `REAL250005045757.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045757 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(F)(F)F 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', 'F', 'F', 'F', '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, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 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] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [180, 124, 124, 124, 55, 36, 10, 11, 1, 11, 1, 1, 1, 1, 1, 1, 180, 180, 180, 180, 180, 180, 180, 180, 124, 55, 55, 36, 36, 11, 1] 180 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 722 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045757 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045757 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045757/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045757 Building REAL250005045758 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045758' /scratch/stefan/7916127/working/building/REAL250005045758 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045758 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045758/0 /scratch/stefan/7916127/working/building/REAL250005045758 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/906 `/scratch/stefan/7916127/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045758.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045758 none CC1=COC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 119, 119, 119, 47, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 186, 186, 186, 186, 186, 119, 47, 47, 30, 30, 9, 1] 186 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]) total number of confs: 506 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045758 none CC1=COC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 6, 4, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 68, 101, 178, 179, 178, 186, 186, 186, 186, 186, 2, 2, 2, 1, 1, 13, 68, 68, 101, 101, 179, 186] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 692 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045758 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045758 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045758/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045758 Building REAL250005045759 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045759' /scratch/stefan/7916127/working/building/REAL250005045759 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045759 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045759/0 /scratch/stefan/7916127/working/building/REAL250005045759 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/907 `/scratch/stefan/7916127/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045759.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045759 none C[C@H]1C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 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', 'N.am', 'C.2', 'O.2', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 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, 104, 201, 104, 104, 49, 30, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 104, 49, 49, 30, 30, 7, 1] 201 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]) total number of confs: 657 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045759 none C[C@H]1C[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 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', 'N.am', 'C.2', 'O.2', '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, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 67, 112, 189, 189, 189, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 67, 67, 112, 112, 189, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045759 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045759 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045759/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045759 Building REAL250005045760 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045760' /scratch/stefan/7916127/working/building/REAL250005045760 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045760 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045760/0 /scratch/stefan/7916127/working/building/REAL250005045760 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/908 `/scratch/stefan/7916127/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CCC1) `REAL250005045760.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045760 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CCC1 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.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 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, 4, 7, 6, 7, 7, 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, 113, 113, 113, 58, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 113, 58, 58, 35, 35, 9, 1, 201, 201, 201, 201, 201, 201] 201 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: 689 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: REAL250005045760 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=CCC1 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.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 7, 7, 7, 44, 79, 189, 189, 189, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 7, 44, 44, 79, 79, 189, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 30, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 699 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045760 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045760 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045760/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045760 Building REAL250005045761 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045761' /scratch/stefan/7916127/working/building/REAL250005045761 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045761 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045761/0 /scratch/stefan/7916127/working/building/REAL250005045761 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/909 `/scratch/stefan/7916127/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045761.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045761 none CN1C(=O)CC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 117, 157, 117, 117, 48, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 157, 117, 48, 48, 33, 33, 10, 1] 157 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: 518 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: REAL250005045761 none CN1C(=O)CC[C@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 72, 147, 147, 147, 157, 157, 157, 157, 157, 2, 2, 2, 1, 1, 1, 1, 9, 42, 42, 72, 72, 147, 157] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 559 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045761 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045761 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045761/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045761 Building REAL250005045762 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045762' /scratch/stefan/7916127/working/building/REAL250005045762 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045762 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045762/0 /scratch/stefan/7916127/working/building/REAL250005045762 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/910 `/scratch/stefan/7916127/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045762.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045762 none CN1N=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 101, 71, 71, 71, 35, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 101, 101, 101, 101, 71, 35, 35, 20, 20, 7, 1] 101 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]) total number of confs: 314 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045762 none CN1N=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 33, 50, 97, 97, 97, 101, 101, 101, 101, 101, 1, 2, 2, 2, 7, 32, 32, 50, 50, 97, 101] 101 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 363 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045762 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045762 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045762/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045762 Building REAL250005045763 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045763' /scratch/stefan/7916127/working/building/REAL250005045763 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045763 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045763/0 /scratch/stefan/7916127/working/building/REAL250005045763 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/911 `/scratch/stefan/7916127/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045763.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045763 none CC1(C)CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 80, 80, 73, 73, 73, 41, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 80, 73, 41, 41, 30, 30, 11, 1] 80 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: 281 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: REAL250005045763 none CC1(C)CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 1, 3, 3, 3, 15, 27, 71, 71, 71, 80, 80, 80, 80, 80, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 15, 15, 27, 27, 71, 80] 80 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 33, 27, 28, 29, 30, 31] set([8, 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: 267 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045763 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045763 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045763/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045763 Building REAL250005045764 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045764' /scratch/stefan/7916127/working/building/REAL250005045764 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045764 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045764/0 /scratch/stefan/7916127/working/building/REAL250005045764 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/912 `/scratch/stefan/7916127/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045764.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045764 none C[C@@H]1OCCO[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 124 conformations in input total number of sets (complete confs): 124 using faster count positions algorithm for large data unique positions, atoms: [124, 124, 124, 124, 124, 124, 124, 108, 124, 108, 108, 40, 25, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 124, 124, 124, 124, 124, 124, 124, 108, 40, 40, 25, 25, 5, 1] 124 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: 410 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: REAL250005045764 none C[C@@H]1OCCO[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 23, 45, 119, 119, 119, 124, 124, 124, 124, 124, 2, 2, 2, 1, 1, 1, 1, 4, 23, 23, 45, 45, 119, 124] 124 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([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: 414 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045764 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045764 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045764/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045764 Building REAL250005045765 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045765' /scratch/stefan/7916127/working/building/REAL250005045765 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045765 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045765/0 /scratch/stefan/7916127/working/building/REAL250005045765 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/913 `/scratch/stefan/7916127/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045765.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045765 none CC[C@@H]1CCO[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 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, 90, 90, 90, 90, 90, 90, 77, 90, 77, 77, 36, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 77, 36, 36, 22, 22, 7, 1] 90 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: 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: REAL250005045765 none CC[C@@H]1CCO[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 34, 85, 85, 85, 90, 90, 90, 90, 90, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 19, 19, 34, 34, 85, 90] 90 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 28, 29, 30, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045765 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045765 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045765/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045765 Building REAL250005045766 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045766' /scratch/stefan/7916127/working/building/REAL250005045766 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045766 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045766/0 /scratch/stefan/7916127/working/building/REAL250005045766 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/914 `/scratch/stefan/7916127/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1C1CC1) `REAL250005045766.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045766 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1C1CC1 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'] 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 107, 107, 107, 46, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 197, 197, 201, 201, 197, 197, 197, 197, 197, 107, 46, 46, 28, 28, 7, 1, 197, 201, 201, 201, 201, 201] 201 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: 653 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045766 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1C1CC1 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'] 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 25, 25, 25, 88, 119, 195, 195, 195, 201, 201, 201, 201, 201, 1, 1, 1, 1, 5, 5, 5, 5, 5, 25, 88, 88, 119, 119, 195, 201, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 742 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045766 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1C1CC1 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'] 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 50, 81, 178, 179, 178, 197, 197, 197, 197, 197, 1, 1, 5, 5, 1, 1, 1, 1, 1, 9, 50, 50, 81, 81, 179, 197, 1, 5, 5, 5, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 33, 17, 18, 21, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38]) total number of confs: 663 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045766 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045766 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045766/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045766 Building REAL250005045767 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045767' /scratch/stefan/7916127/working/building/REAL250005045767 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045767 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045767/0 /scratch/stefan/7916127/working/building/REAL250005045767 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/915 `/scratch/stefan/7916127/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCC12CC2)C1=CC(=O)[N-]O1) `REAL250005045767.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045767 none O=C(NCCNC(=O)C1CCCC12CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 29, 44, 106, 106, 106, 138, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 9, 29, 29, 44, 44, 106, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 138, 1] 138 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: 475 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: REAL250005045767 none O=C(NCCNC(=O)C1CCCC12CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 57, 32, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 130, 138, 138, 138, 138, 138, 130, 57, 57, 32, 32, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 138] 138 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 463 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045767 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045767 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045767/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045767 Building REAL250005045768 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045768' /scratch/stefan/7916127/working/building/REAL250005045768 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045768 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045768/0 /scratch/stefan/7916127/working/building/REAL250005045768 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/916 `/scratch/stefan/7916127/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1) `REAL250005045768.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045768 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1 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', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 83, 83, 83, 42, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 139, 139, 139, 139, 139, 139, 83, 42, 42, 30, 30, 11, 1, 139, 139] 139 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]) total number of confs: 382 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045768 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NC=N1 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', 'N.pl3', 'C.2', 'N.2', '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, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 45, 72, 131, 131, 131, 139, 139, 139, 139, 139, 1, 1, 1, 2, 2, 2, 10, 44, 44, 72, 72, 131, 139, 1, 1] 139 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 525 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045768 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045768 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045768/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045768 Building REAL250005045769 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045769' /scratch/stefan/7916127/working/building/REAL250005045769 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045769 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045769/0 /scratch/stefan/7916127/working/building/REAL250005045769 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/917 `/scratch/stefan/7916127/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045769.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045769 none CC1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 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, 160, 42, 42, 42, 22, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 42, 22, 22, 15, 15, 4, 1, 201, 201] 201 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: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045769 none CC1CCC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 34, 34, 34, 115, 135, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 34, 115, 115, 135, 135, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 20, 24, 25, 26, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 733 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045769 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045769 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045769/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045769 Building REAL250005045770 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045770' /scratch/stefan/7916127/working/building/REAL250005045770 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045770 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045770/0 /scratch/stefan/7916127/working/building/REAL250005045770 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/918 `/scratch/stefan/7916127/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)N=C1) `REAL250005045770.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045770 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)N=C1 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', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 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, 41, 26, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 114, 41, 41, 26, 26, 6, 1, 201, 201, 201, 201] 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: 506 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: REAL250005045770 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N(C)N=C1 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', 'N.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 56, 94, 197, 197, 197, 201, 201, 201, 201, 201, 1, 1, 1, 1, 2, 2, 2, 11, 56, 56, 94, 94, 197, 201, 2, 2, 2, 1] 201 rigid atoms, others: [0, 1, 2, 3, 34, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 732 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045770 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045770 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045770/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045770 Building REAL250005045771 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045771' /scratch/stefan/7916127/working/building/REAL250005045771 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045771 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045771/0 /scratch/stefan/7916127/working/building/REAL250005045771 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/919 `/scratch/stefan/7916127/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045771.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045771 none CC(C)C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 180, 201, 107, 181, 107, 107, 34, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 181, 107, 34, 34, 21, 21, 4, 1] 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]) total number of confs: 808 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045771 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045771 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045771/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045771 Building REAL250005045772 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045772' /scratch/stefan/7916127/working/building/REAL250005045772 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045772 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045772/0 /scratch/stefan/7916127/working/building/REAL250005045772 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/920 `/scratch/stefan/7916127/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045772.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045772 none CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 190, 92, 92, 92, 31, 18, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 190, 190, 190, 201, 201, 201, 201, 201, 201, 201, 92, 31, 31, 18, 18, 4, 1, 190, 190, 190, 190, 190, 190] 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: 684 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: REAL250005045772 none CCCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['C.3', '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', 'H', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 7, 7, 7, 44, 71, 184, 185, 185, 190, 190, 190, 190, 190, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 7, 44, 44, 71, 71, 185, 190, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 2, 3, 4, 37, 38, 39, 40, 18, 19, 20, 36] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 654 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045772 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045772 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045772/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045772 Building REAL250005045773 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045773' /scratch/stefan/7916127/working/building/REAL250005045773 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045773 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045773/0 /scratch/stefan/7916127/working/building/REAL250005045773 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/921 `/scratch/stefan/7916127/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045773.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045773 none C=CC(C)C(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 174 conformations in input total number of sets (complete confs): 174 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 148, 174, 80, 148, 80, 80, 35, 24, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 174, 174, 148, 148, 148, 148, 80, 35, 35, 24, 24, 4, 1] 174 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: 720 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045773 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045773 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045773/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045773 Building REAL250005045774 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045774' /scratch/stefan/7916127/working/building/REAL250005045774 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045774 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045774/0 /scratch/stefan/7916127/working/building/REAL250005045774 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/922 `/scratch/stefan/7916127/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045774.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045774 none CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 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', 'H', '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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need 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, 77, 77, 77, 40, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 195, 195, 195, 201, 201, 201, 201, 201, 77, 40, 40, 25, 25, 7, 1, 195, 195, 195, 195, 195, 195] 201 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: 641 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045774 none CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 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', 'H', '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, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 7, 7, 7, 47, 80, 188, 193, 193, 195, 195, 195, 195, 195, 1, 1, 1, 3, 3, 3, 3, 3, 7, 47, 47, 80, 80, 193, 195, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 1, 2, 3, 36, 37, 35, 33, 34, 17, 18, 19] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045774 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045774 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045774/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045774 Building REAL250005045775 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045775' /scratch/stefan/7916127/working/building/REAL250005045775 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045775 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045775/0 /scratch/stefan/7916127/working/building/REAL250005045775 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/923 `/scratch/stefan/7916127/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CC2(CCC2)C1)C1=CC(=O)[N-]O1) `REAL250005045775.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045775 none O=C(NCCNC(=O)C1CC2(CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 30, 50, 118, 118, 118, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 30, 30, 50, 50, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 651 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: REAL250005045775 none O=C(NCCNC(=O)C1CC2(CCC2)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [193, 193, 112, 67, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 112, 112, 67, 67, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 748 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045775 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045775 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045775/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045775 Building REAL250005045776 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045776' /scratch/stefan/7916127/working/building/REAL250005045776 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045776 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045776/0 /scratch/stefan/7916127/working/building/REAL250005045776 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/924 `/scratch/stefan/7916127/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC#CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045776.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045776 none CC#CCCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 123, 99, 35, 35, 35, 17, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 190, 190, 141, 141, 99, 99, 35, 17, 17, 10, 10, 2, 1] 201 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: 972 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045776 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045776 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045776/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045776 Building REAL250005045777 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045777' /scratch/stefan/7916127/working/building/REAL250005045777 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045777 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045777/0 /scratch/stefan/7916127/working/building/REAL250005045777 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/925 `/scratch/stefan/7916127/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1[C@@H]2COC[C@@H]21)C1=CC(=O)[N-]O1) `REAL250005045777.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045777 none O=C(NCCNC(=O)[C@H]1[C@@H]2COC[C@@H]21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 34, 50, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 8, 33, 33, 50, 50, 113, 201, 201, 201, 201, 1] 201 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: 650 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045777 none O=C(NCCNC(=O)[C@H]1[C@@H]2COC[C@@H]21)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', '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, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 116, 74, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 189, 201, 201, 201, 201, 201, 189, 116, 116, 74, 74, 13, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 33, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 752 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045777 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045777 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045777/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045777 Building REAL250005045778 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045778' /scratch/stefan/7916127/working/building/REAL250005045778 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045778 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045778/0 /scratch/stefan/7916127/working/building/REAL250005045778 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/926 `/scratch/stefan/7916127/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CCCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045778.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045778 none O=C(CCCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 97, 109, 147, 201, 201, 19, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 97, 97, 127, 127, 153, 153, 201, 201, 201, 201, 201, 31, 19, 19, 11, 11, 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: 1003 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045778 none O=C(CCCC1CC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 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, 7, 7, 7] 0 hydrogens 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, 11, 7, 3, 1, 1, 1, 1, 53, 53, 157, 179, 201, 201, 201, 201, 201, 201, 201, 201, 11, 11, 7, 7, 3, 3, 1, 1, 1, 1, 1, 53, 157, 157, 179, 179, 201, 201] 201 rigid atoms, others: [4, 5, 6, 7, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 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: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045778 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045778 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045778/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045778 Building REAL250005045779 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045779' /scratch/stefan/7916127/working/building/REAL250005045779 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045779 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045779/0 /scratch/stefan/7916127/working/building/REAL250005045779 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/927 `/scratch/stefan/7916127/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1=O) `REAL250005045779.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045779 none CN1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 201 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, 129, 129, 129, 51, 35, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 51, 51, 35, 35, 9, 1] 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]) total number of confs: 647 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045779 none CN1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', '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.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens 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, 11, 11, 11, 61, 106, 190, 194, 190, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 11, 61, 61, 106, 106, 194, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 751 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045779 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045779 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045779/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045779 Building REAL250005045780 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045780' /scratch/stefan/7916127/working/building/REAL250005045780 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045780 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045780/0 /scratch/stefan/7916127/working/building/REAL250005045780 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/928 `/scratch/stefan/7916127/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(OCC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045780.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045780 none CCCC(OCC)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens 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, 178, 87, 49, 87, 104, 106, 49, 49, 20, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 191, 181, 181, 87, 106, 106, 106, 106, 106, 49, 20, 20, 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: 943 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045780 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045780 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045780/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045780 Building REAL250005045781 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045781' /scratch/stefan/7916127/working/building/REAL250005045781 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045781 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045781/0 /scratch/stefan/7916127/working/building/REAL250005045781 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/929 `/scratch/stefan/7916127/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045781.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045781 none CC1(C)CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 134, 114, 114, 114, 55, 33, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 114, 55, 55, 33, 33, 10, 1] 134 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: 462 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: REAL250005045781 none CC1(C)CCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 34, 62, 124, 124, 124, 134, 134, 134, 134, 134, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 7, 34, 34, 62, 62, 124, 134] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 26, 27, 28, 29, 30] set([7, 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: 483 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045781 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045781 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045781/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045781 Building REAL250005045782 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045782' /scratch/stefan/7916127/working/building/REAL250005045782 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045782 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045782/0 /scratch/stefan/7916127/working/building/REAL250005045782 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/930 `/scratch/stefan/7916127/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045782.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045782 none CC1=COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 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, 75, 75, 75, 37, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 75, 37, 37, 24, 24, 9, 1, 87] 87 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]) total number of confs: 282 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045782 none CC1=COC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 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, 6, 6, 7, 27, 43, 79, 79, 79, 87, 87, 87, 87, 87, 1, 2, 2, 2, 1, 7, 27, 27, 43, 43, 79, 87, 1] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 319 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045782 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045782 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045782/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045782 Building REAL250005045783 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045783' /scratch/stefan/7916127/working/building/REAL250005045783 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045783 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045783/0 /scratch/stefan/7916127/working/building/REAL250005045783 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/931 `/scratch/stefan/7916127/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC(=O)N1) `REAL250005045783.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045783 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 60, 95, 145, 145, 145, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 10, 60, 60, 95, 95, 145, 160, 1, 1] 160 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045783 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CSC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 14, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 36, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 97, 160, 160, 160, 160, 160, 97, 36, 36, 27, 27, 9, 1, 160, 160] 160 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]) total number of confs: 400 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045783 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045783 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045783/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045783 Building REAL250005045784 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045784' /scratch/stefan/7916127/working/building/REAL250005045784 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045784 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045784/0 /scratch/stefan/7916127/working/building/REAL250005045784 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/932 `/scratch/stefan/7916127/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(CC)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045784.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045784 none C=CC(CC)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 185, 119, 185, 201, 45, 45, 45, 20, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 193, 193, 193, 185, 201, 201, 201, 201, 201, 119, 119, 45, 20, 20, 13, 13, 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: 942 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045784 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045784 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045784/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045784 Building REAL250005045785 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045785' /scratch/stefan/7916127/working/building/REAL250005045785 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045785 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045785/0 /scratch/stefan/7916127/working/building/REAL250005045785 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/933 `/scratch/stefan/7916127/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1) `REAL250005045785.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045785 none CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', 'H', '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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 30, 30, 30, 101, 126, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 11, 11, 11, 11, 11, 11, 30, 101, 101, 126, 126, 201, 201, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 34, 35, 36, 37, 33, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 763 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: REAL250005045785 none CC(C)(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C1CC1 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', 'H', '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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 60, 131, 60, 60, 26, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 130, 201, 201, 131, 130, 131, 131, 131, 131, 60, 26, 26, 16, 16, 4, 1, 201, 201, 201, 201, 201] 201 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]) total number of confs: 809 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045785 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045785 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045785/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045785 Building REAL250005045786 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045786' /scratch/stefan/7916127/working/building/REAL250005045786 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045786 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045786/0 /scratch/stefan/7916127/working/building/REAL250005045786 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/934 `/scratch/stefan/7916127/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@H]1C[C@H]2C[C@H]2C1)C1=CC(=O)[N-]O1) `REAL250005045786.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045786 none O=C(NCCNC(=O)[C@H]1C[C@H]2C[C@H]2C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 7, 31, 45, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 31, 31, 45, 45, 118, 201, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 35, 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]) total number of confs: 640 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: REAL250005045786 none O=C(NCCNC(=O)[C@H]1C[C@H]2C[C@H]2C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', '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.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: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [191, 187, 109, 66, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 187, 201, 201, 201, 201, 201, 191, 109, 109, 66, 66, 13, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 737 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045786 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045786 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045786/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045786 Building REAL250005045787 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045787' /scratch/stefan/7916127/working/building/REAL250005045787 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045787 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045787/0 /scratch/stefan/7916127/working/building/REAL250005045787 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/935 `/scratch/stefan/7916127/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CON=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045787.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045787 none O=C(CC1=CON=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [46, 46, 46, 85, 201, 201, 201, 201, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 85, 85, 201, 201, 46, 21, 21, 14, 14, 4, 1] 201 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]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045787 none O=C(CC1=CON=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.3', 'N.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 12, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 4, 1, 1, 1, 1, 1, 1, 17, 17, 84, 110, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 1, 1, 17, 84, 84, 110, 110, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22, 23] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 746 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045787 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045787 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045787/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045787 Building REAL250005045788 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045788' /scratch/stefan/7916127/working/building/REAL250005045788 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045788 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045788/0 /scratch/stefan/7916127/working/building/REAL250005045788 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/936 `/scratch/stefan/7916127/working/3D/936' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045788.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045788 none CN1C(=O)CC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 157, 157, 157, 157, 157, 117, 157, 117, 117, 47, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 157, 157, 157, 157, 157, 157, 157, 117, 47, 47, 34, 34, 10, 1] 157 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: 516 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: REAL250005045788 none CN1C(=O)CC[C@@H]1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 42, 72, 147, 147, 147, 157, 157, 157, 157, 157, 2, 2, 2, 1, 1, 1, 1, 9, 42, 42, 72, 72, 147, 157] 157 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 559 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045788 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045788 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045788/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045788 Building REAL250005045789 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045789' /scratch/stefan/7916127/working/building/REAL250005045789 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045789 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045789/0 /scratch/stefan/7916127/working/building/REAL250005045789 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/937 `/scratch/stefan/7916127/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045789.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045789 none CC1(C)CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 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, 147, 47, 47, 47, 24, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 47, 24, 24, 16, 16, 4, 1, 201, 201] 201 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: 787 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045789 none CC1(C)CC(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 35, 35, 35, 114, 133, 201, 201, 201, 201, 201, 201, 201, 201, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 6, 6, 35, 114, 114, 133, 133, 201, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 40, 20, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 748 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045789 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045789 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045789/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045789 Building REAL250005045790 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045790' /scratch/stefan/7916127/working/building/REAL250005045790 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045790 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045790/0 /scratch/stefan/7916127/working/building/REAL250005045790 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/938 `/scratch/stefan/7916127/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(F)CCOC1)C1=CC(=O)[N-]O1) `REAL250005045790.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045790 none O=C(NCCNC(=O)C1(F)CCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 31, 42, 101, 101, 101, 166, 166, 166, 166, 166, 1, 1, 1, 1, 1, 1, 9, 31, 31, 42, 42, 101, 166, 166, 166, 166, 166, 166, 1] 166 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 561 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: REAL250005045790 none O=C(NCCNC(=O)C1(F)CCOC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [157, 157, 81, 58, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 157, 166, 166, 166, 166, 166, 157, 81, 81, 58, 58, 10, 1, 1, 1, 1, 1, 1, 166] 166 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 591 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045790 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045790 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045790/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045790 Building REAL250005045791 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045791' /scratch/stefan/7916127/working/building/REAL250005045791 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045791 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045791/0 /scratch/stefan/7916127/working/building/REAL250005045791 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/939 `/scratch/stefan/7916127/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1C) `REAL250005045791.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045791 none CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 141, 141, 141, 103, 103, 103, 43, 25, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 141, 141, 141, 141, 141, 141, 103, 43, 43, 25, 25, 7, 1, 141, 141, 141] 141 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: 405 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045791 none CC1=NC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 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, 8, 8, 8, 49, 85, 137, 137, 137, 141, 141, 141, 141, 141, 1, 1, 2, 2, 2, 1, 8, 49, 49, 85, 85, 137, 141, 2, 2, 2] 141 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 543 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045791 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045791 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045791/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045791 Building REAL250005045792 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045792' /scratch/stefan/7916127/working/building/REAL250005045792 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045792 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045792/0 /scratch/stefan/7916127/working/building/REAL250005045792 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/940 `/scratch/stefan/7916127/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)C) `REAL250005045792.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045792 none CC(C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)C(C)(C)C 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', '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, 6, 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, 4, 7, 6, 7, 7, 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 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 88, 88, 88, 45, 29, 9, 10, 1, 10, 1, 1, 1, 1, 1, 1, 115, 116, 116, 115, 116, 116, 116, 116, 88, 45, 45, 29, 29, 10, 1, 116, 116, 116, 116, 116, 116, 116, 116, 116] 116 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 476 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045792 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045792 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045792/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045792 Building REAL250005045793 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045793' /scratch/stefan/7916127/working/building/REAL250005045793 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045793 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045793/0 /scratch/stefan/7916127/working/building/REAL250005045793 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/941 `/scratch/stefan/7916127/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C12CCC(CC1)C2)C1=CC(=O)[N-]O1) `REAL250005045793.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045793 none O=C(NCCNC(=O)C12CCC(CC1)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [7, 1, 7, 7, 30, 48, 91, 91, 91, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 7, 30, 30, 48, 48, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 498 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045793 none O=C(NCCNC(=O)C12CCC(CC1)C2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.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, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [193, 193, 88, 47, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 193, 201, 201, 201, 201, 201, 193, 88, 88, 47, 47, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045793 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045793 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045793/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045793 Building REAL250005045794 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045794' /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045794 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045794/0 /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/942 `/scratch/stefan/7916127/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045794.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045794 none C[N@@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 7, 1] 17 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: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045794 none C[N@@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 12, 13, 13, 13, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 12, 12, 13, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 32, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045794/1 /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/943 `/scratch/stefan/7916127/working/3D/943' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045794.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045794 none C[N@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 10, 10, 10, 6, 1] 16 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: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045794 none C[N@H+]1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 12, 13, 13, 13, 16, 16, 16, 16, 16, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 12, 12, 13, 16] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 32, 25, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045794/2 /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/944 `/scratch/stefan/7916127/working/3D/944' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045794.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045794/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045794 none CN1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', '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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 86, 86, 86, 43, 29, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 86, 43, 43, 29, 29, 8, 1] 93 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: 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: REAL250005045794 none CN1CCCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', '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', '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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 30, 47, 88, 88, 88, 93, 93, 93, 93, 93, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30, 30, 47, 47, 88, 93] 93 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045794 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045794 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045794/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045794/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045794/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045794 Building REAL250005045795 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045795' /scratch/stefan/7916127/working/building/REAL250005045795 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045795 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045795/0 /scratch/stefan/7916127/working/building/REAL250005045795 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/945 `/scratch/stefan/7916127/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045795.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045795 none CC1=CC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 121, 121, 121, 57, 40, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 121, 57, 57, 40, 40, 11, 1, 201] 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]) total number of confs: 534 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: REAL250005045795 none CC1=CC(C)=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', '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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 98, 189, 189, 189, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 2, 2, 2, 11, 58, 58, 98, 98, 189, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 35, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 734 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045795 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045795 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045795/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045795 Building REAL250005045796 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045796' /scratch/stefan/7916127/working/building/REAL250005045796 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045796 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045796/0 /scratch/stefan/7916127/working/building/REAL250005045796 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/946 `/scratch/stefan/7916127/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CC=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045796.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045796 none O=C(CC1=CC=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 125, 201, 201, 201, 201, 201, 21, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 125, 125, 201, 201, 201, 201, 63, 21, 21, 16, 16, 4, 1] 201 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]) total number of confs: 613 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045796 none O=C(CC1=CC=CN=C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 7, 1, 1, 1, 1, 1, 1, 1, 17, 17, 94, 116, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 17, 94, 94, 116, 116, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 739 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045796 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045796 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045796/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045796 Building REAL250005045797 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045797' /scratch/stefan/7916127/working/building/REAL250005045797 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045797 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045797/0 /scratch/stefan/7916127/working/building/REAL250005045797 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/947 `/scratch/stefan/7916127/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045797.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045797 none CCC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 147, 147, 147, 147, 123, 123, 123, 40, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 146, 147, 123, 40, 40, 27, 27, 7, 1] 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]) total number of confs: 737 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045797 none CCC1=CC=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', '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', '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, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 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: [9, 1, 1, 1, 1, 1, 1, 8, 8, 9, 34, 54, 135, 135, 135, 147, 147, 147, 147, 147, 1, 9, 9, 9, 9, 9, 1, 1, 9, 34, 34, 54, 54, 135, 147] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 20, 26, 27] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045797 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045797 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045797/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045797 Building REAL250005045798 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045798' /scratch/stefan/7916127/working/building/REAL250005045798 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045798 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045798/0 /scratch/stefan/7916127/working/building/REAL250005045798 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/948 `/scratch/stefan/7916127/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(F)(F)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045798.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045798 none CC(F)(F)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [141, 91, 138, 138, 118, 73, 73, 73, 37, 30, 12, 13, 1, 13, 1, 1, 1, 1, 1, 1, 141, 141, 141, 121, 121, 119, 119, 73, 37, 37, 30, 30, 13, 1] 141 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]) total number of confs: 759 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045798 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045798 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045798/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045798 Building REAL250005045799 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045799' /scratch/stefan/7916127/working/building/REAL250005045799 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045799 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045799/0 /scratch/stefan/7916127/working/building/REAL250005045799 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/949 `/scratch/stefan/7916127/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCC(=O)NC1)C1=CC(=O)[N-]O1) `REAL250005045799.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045799 none O=C(NCCNC(=O)C1CCC(=O)NC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 34, 50, 117, 117, 117, 200, 200, 200, 200, 200, 200, 1, 1, 1, 1, 1, 1, 10, 34, 34, 50, 50, 117, 200, 200, 200, 200, 200, 200, 200, 200, 1] 200 rigid atoms, others: [1, 35, 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]) total number of confs: 667 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: REAL250005045799 none O=C(NCCNC(=O)C1CCC(=O)NC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 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 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 100, 63, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 182, 200, 200, 200, 200, 200, 182, 100, 100, 63, 63, 12, 1, 1, 1, 1, 1, 1, 1, 1, 200] 200 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 719 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045799 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045799 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045799/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045799 Building REAL250005045800 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045800' /scratch/stefan/7916127/working/building/REAL250005045800 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045800 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045800/0 /scratch/stefan/7916127/working/building/REAL250005045800 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/950 `/scratch/stefan/7916127/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045800.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045800 none CCC1=NNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens 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, 149, 149, 149, 149, 149, 103, 103, 103, 44, 30, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 200, 201, 201, 201, 201, 149, 149, 103, 44, 44, 30, 30, 9, 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: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045800 none CCC1=NNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 41, 59, 141, 141, 141, 149, 149, 149, 149, 149, 6, 6, 6, 5, 5, 1, 1, 8, 41, 41, 59, 59, 141, 149] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27] set([0, 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: 520 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045800 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045800 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045800/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045800 Building REAL250005045801 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045801' /scratch/stefan/7916127/working/building/REAL250005045801 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045801 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045801/0 /scratch/stefan/7916127/working/building/REAL250005045801 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/951 `/scratch/stefan/7916127/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NNN=C1) `REAL250005045801.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045801 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 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: [5, 1, 5, 5, 17, 32, 67, 67, 67, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 5, 17, 17, 32, 32, 67, 71, 1, 1] 71 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 247 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045801 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=NNN=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 8, 1, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [6, 7, 4, 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] 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: [69, 69, 41, 28, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 69, 71, 71, 71, 71, 69, 41, 41, 28, 28, 7, 1, 71, 71] 71 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045801 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045801/1 /scratch/stefan/7916127/working/building/REAL250005045801 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/952 `/scratch/stefan/7916127/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CN=NN1) `REAL250005045801.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045801 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CN=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 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: [9, 1, 9, 9, 30, 44, 81, 81, 81, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 9, 30, 30, 44, 44, 81, 91, 1, 1] 91 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 317 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045801 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CN=NN1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 8, 8, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 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: [78, 78, 39, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 78, 91, 91, 91, 91, 78, 39, 39, 24, 24, 9, 1, 91, 91] 91 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27]) total number of confs: 306 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045801 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045801 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045801/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045801/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045801 Building REAL250005045802 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045802' /scratch/stefan/7916127/working/building/REAL250005045802 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045802 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045802/0 /scratch/stefan/7916127/working/building/REAL250005045802 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/953 `/scratch/stefan/7916127/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1C) `REAL250005045802.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045802 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 63, 63, 63, 31, 20, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 63, 31, 31, 20, 20, 5, 1, 65, 65, 65] 65 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]) 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: REAL250005045802 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', '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', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 4, 21, 35, 63, 63, 63, 65, 65, 65, 65, 65, 1, 1, 1, 2, 2, 2, 1, 5, 21, 21, 35, 35, 63, 65, 2, 2, 2] 65 rigid atoms, others: [0, 1, 2, 3, 4, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045802 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045802 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045802/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045802 Building REAL250005045803 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045803' /scratch/stefan/7916127/working/building/REAL250005045803 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045803 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045803/0 /scratch/stefan/7916127/working/building/REAL250005045803 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/954 `/scratch/stefan/7916127/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN=N1) `REAL250005045803.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045803 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 57, 57, 57, 37, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 113, 113, 113, 113, 113, 113, 113, 57, 37, 37, 26, 26, 9, 1, 113] 113 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]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045803 none CC1=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=CN=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 33, 55, 107, 107, 107, 113, 113, 113, 113, 113, 1, 1, 1, 2, 2, 2, 1, 5, 33, 33, 55, 55, 107, 113, 1] 113 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 20, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 413 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045803 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045803 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045803/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045803 Building REAL250005045804 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045804' /scratch/stefan/7916127/working/building/REAL250005045804 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045804 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045804/0 /scratch/stefan/7916127/working/building/REAL250005045804 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/955 `/scratch/stefan/7916127/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC=C1O)C1=CC(=O)[N-]O1) `REAL250005045804.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045804 none O=C(NCCNC(=O)C1=CC=CC=C1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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 292 conformations in input total number of sets (complete confs): 292 using faster count positions algorithm for large data unique positions, atoms: [8, 1, 8, 8, 28, 43, 95, 95, 95, 146, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 8, 28, 28, 43, 43, 95, 146, 146, 146, 146, 292, 1] 292 rigid atoms, others: [32, 1, 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]) total number of confs: 691 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: REAL250005045804 none O=C(NCCNC(=O)C1=CC=CC=C1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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 292 conformations in input total number of sets (complete confs): 292 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 66, 44, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 142, 146, 146, 146, 146, 146, 142, 66, 66, 44, 44, 10, 1, 1, 1, 1, 2, 146] 292 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 520 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045804 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045804 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045804/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045804 Building REAL250005045805 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045805' /scratch/stefan/7916127/working/building/REAL250005045805 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045805 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045805/0 /scratch/stefan/7916127/working/building/REAL250005045805 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/956 `/scratch/stefan/7916127/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=CC(O)=C1)C1=CC(=O)[N-]O1) `REAL250005045805.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045805 none O=C(NCCNC(=O)C1=CC=CC(O)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 352 conformations in input total number of sets (complete confs): 352 using faster count positions algorithm for large data unique positions, atoms: [10, 1, 10, 10, 32, 53, 99, 99, 99, 176, 176, 176, 176, 176, 176, 1, 1, 1, 1, 1, 1, 10, 32, 32, 53, 53, 99, 176, 176, 176, 352, 176, 1] 352 rigid atoms, others: [32, 1, 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]) total number of confs: 832 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045805 none O=C(NCCNC(=O)C1=CC=CC(O)=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.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, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 352 conformations in input total number of sets (complete confs): 352 using faster count positions algorithm for large data unique positions, atoms: [160, 160, 73, 36, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 160, 176, 176, 176, 176, 176, 160, 73, 73, 36, 36, 7, 1, 1, 1, 2, 1, 176] 352 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045805 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045805 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045805/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045805 Building REAL250005045806 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045806' /scratch/stefan/7916127/working/building/REAL250005045806 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045806 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045806/0 /scratch/stefan/7916127/working/building/REAL250005045806 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/957 `/scratch/stefan/7916127/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045806.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045806 none NC(=O)C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 4, 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 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 91, 105, 91, 67, 67, 67, 32, 27, 11, 12, 1, 12, 1, 1, 1, 1, 1, 1, 105, 105, 91, 91, 67, 32, 32, 27, 27, 12, 1] 105 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]) total number of confs: 347 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045806 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045806 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045806/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045806 Building REAL250005045807 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045807' /scratch/stefan/7916127/working/building/REAL250005045807 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045807 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045807/0 /scratch/stefan/7916127/working/building/REAL250005045807 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/958 `/scratch/stefan/7916127/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045807.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045807 none NC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 169, 169, 169, 101, 101, 101, 45, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 169, 169, 169, 169, 169, 101, 45, 45, 28, 28, 8, 1] 169 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: 464 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045807 none NC1=NC=CC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 3, 7, 7, 7, 7, 7, 6, 4, 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 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 52, 83, 165, 165, 165, 169, 169, 169, 169, 169, 2, 2, 1, 1, 1, 10, 52, 52, 83, 83, 165, 169] 169 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045807 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045807 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045807/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045807 Building REAL250005045808 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045808' /scratch/stefan/7916127/working/building/REAL250005045808 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045808 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045808/0 /scratch/stefan/7916127/working/building/REAL250005045808 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/959 `/scratch/stefan/7916127/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045808.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045808 none NC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 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 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 37, 27, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 37, 37, 27, 27, 8, 1] 73 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]) 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: REAL250005045808 none NC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 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 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, 4, 4, 4, 19, 33, 70, 70, 70, 73, 73, 73, 73, 73, 1, 1, 1, 1, 4, 19, 19, 33, 33, 70, 73] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045808 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045808 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045808/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045808 Building REAL250005045809 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045809' /scratch/stefan/7916127/working/building/REAL250005045809 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045809 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045809/0 /scratch/stefan/7916127/working/building/REAL250005045809 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/960 `/scratch/stefan/7916127/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC=C[N+]([O-])=C1)C1=CC(=O)[N-]O1) `REAL250005045809.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045809 none O=C(NCCNC(=O)C1=CC=C[N+]([O-])=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 3, 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: [11, 1, 11, 11, 28, 37, 72, 72, 72, 123, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 11, 28, 28, 37, 37, 72, 123, 123, 123, 123, 1] 123 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 326 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045809 none O=C(NCCNC(=O)C1=CC=C[N+]([O-])=C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', '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, 5, 8, 1, 11, 1, 1, 1, 1, 8, 12, 1, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 3, 7, 3, 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: [114, 114, 59, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 114, 123, 123, 123, 123, 123, 114, 59, 59, 37, 37, 7, 1, 1, 1, 1, 123] 123 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045809 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045809 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045809/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045809 Building REAL250005045810 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045810' /scratch/stefan/7916127/working/building/REAL250005045810 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045810 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045810/0 /scratch/stefan/7916127/working/building/REAL250005045810 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/961 `/scratch/stefan/7916127/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045810.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045810 none COC(=O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 6, 4, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 73, 99, 57, 57, 57, 23, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 99, 99, 99, 73, 73, 57, 23, 23, 20, 20, 4, 1] 99 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]) total number of confs: 370 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045810 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045810 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045810/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045810 Building REAL250005045811 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045811' /scratch/stefan/7916127/working/building/REAL250005045811 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045811 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045811/0 /scratch/stefan/7916127/working/building/REAL250005045811 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/962 `/scratch/stefan/7916127/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)NC=N1)C1=CC(=O)[N-]O1) `REAL250005045811.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045811 none O=C(NCCNC(=O)C1=CC(=O)NC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 22, 33, 69, 69, 69, 87, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 7, 22, 22, 33, 33, 69, 87, 87, 87, 1] 87 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 264 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045811 none O=C(NCCNC(=O)C1=CC(=O)NC=N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 3, 7, 3, 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: [85, 85, 59, 45, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 85, 87, 87, 87, 87, 87, 85, 59, 59, 45, 45, 11, 1, 1, 1, 87] 87 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 325 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045811 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045811 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045811/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045811 Building REAL250005045812 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045812' /scratch/stefan/7916127/working/building/REAL250005045812 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045812 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045812/0 /scratch/stefan/7916127/working/building/REAL250005045812 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/963 `/scratch/stefan/7916127/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045812.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045812 none C#CCSCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 14, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 163, 101, 49, 49, 49, 19, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 101, 101, 49, 19, 19, 10, 10, 2, 1] 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]) total number of confs: 725 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045812 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045812 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045812/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045812 Building REAL250005045813 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045813' /scratch/stefan/7916127/working/building/REAL250005045813 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045813 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045813/0 /scratch/stefan/7916127/working/building/REAL250005045813 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/964 `/scratch/stefan/7916127/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSC=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045813.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045813 none CSC=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'S.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 173, 173, 91, 91, 91, 37, 24, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 173, 173, 91, 37, 37, 24, 24, 6, 1] 201 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]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045813 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045813 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045813/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045813 Building REAL250005045814 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045814' /scratch/stefan/7916127/working/building/REAL250005045814 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045814 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045814/0 /scratch/stefan/7916127/working/building/REAL250005045814 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/965 `/scratch/stefan/7916127/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CNC=CC1=O)C1=CC(=O)[N-]O1) `REAL250005045814.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045814 none O=C(NCCNC(=O)C1=CNC=CC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 33, 45, 109, 109, 109, 158, 158, 158, 158, 158, 158, 1, 1, 1, 1, 1, 1, 9, 33, 33, 45, 45, 109, 158, 158, 158, 158, 1] 158 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) 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: REAL250005045814 none O=C(NCCNC(=O)C1=CNC=CC1=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.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: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [154, 152, 92, 69, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 152, 158, 158, 158, 158, 158, 154, 92, 92, 69, 69, 13, 1, 1, 1, 1, 158] 158 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045814 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045814 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045814/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045814 Building REAL250005045815 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045815' /scratch/stefan/7916127/working/building/REAL250005045815 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045815 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045815/0 /scratch/stefan/7916127/working/building/REAL250005045815 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/966 `/scratch/stefan/7916127/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CS1) `REAL250005045815.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045815 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 139, 139, 139, 57, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 139, 57, 57, 34, 34, 9, 1, 177, 177] 177 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: 589 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045815 none CC1=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.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', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 57, 94, 167, 169, 167, 177, 177, 177, 177, 177, 1, 1, 2, 2, 2, 1, 10, 57, 57, 94, 94, 169, 177, 1, 1] 177 rigid atoms, others: [0, 1, 2, 3, 4, 32, 18, 19, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 660 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045815 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045815 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045815/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045815 Building REAL250005045816 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045816' /scratch/stefan/7916127/working/building/REAL250005045816 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045816 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045816/0 /scratch/stefan/7916127/working/building/REAL250005045816 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/967 `/scratch/stefan/7916127/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)(F)F) `REAL250005045816.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045816 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)C(F)(F)F NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'O.2', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 5, 15, 15, 15, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 64, 40, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 142, 199, 199, 199, 199, 199, 142, 64, 64, 40, 40, 9, 1] 199 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]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045816 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045816 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045816/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045816 Building REAL250005045817 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045817' /scratch/stefan/7916127/working/building/REAL250005045817 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045817 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045817/0 /scratch/stefan/7916127/working/building/REAL250005045817 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/968 `/scratch/stefan/7916127/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045817.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045817 none CCC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 179, 116, 179, 60, 60, 60, 21, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 116, 116, 201, 201, 201, 201, 201, 60, 21, 21, 13, 13, 4, 1, 116, 116, 116, 116] 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: 694 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045817 none CCC(=O)C1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens 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, 5, 1, 5, 1, 1, 7, 7, 7, 38, 55, 105, 106, 105, 116, 116, 116, 116, 116, 1, 1, 24, 24, 24, 24, 24, 7, 38, 38, 55, 55, 106, 116, 1, 1, 1, 1] 201 rigid atoms, others: [33, 2, 35, 4, 5, 34, 19, 20, 36] set([0, 1, 3, 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]) total number of confs: 484 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045817 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045817 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045817/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045817 Building REAL250005045818 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045818' /scratch/stefan/7916127/working/building/REAL250005045818 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045818 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045818/0 /scratch/stefan/7916127/working/building/REAL250005045818 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/969 `/scratch/stefan/7916127/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CO)CCC1)C1=CC(=O)[N-]O1) `REAL250005045818.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045818 none O=C(NCCNC(=O)C1(CO)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [4, 1, 4, 3, 23, 36, 87, 87, 87, 175, 201, 175, 175, 175, 1, 1, 1, 1, 1, 1, 4, 23, 23, 36, 36, 87, 201, 201, 603, 175, 175, 175, 175, 175, 175, 1] 603 rigid atoms, others: [1, 35, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 1328 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045818 none O=C(NCCNC(=O)C1(CO)CCC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 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] 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: [167, 163, 62, 39, 6, 6, 1, 6, 1, 1, 7, 1, 1, 1, 167, 175, 175, 175, 175, 175, 167, 62, 62, 39, 39, 6, 7, 7, 21, 1, 1, 1, 1, 1, 1, 175] 603 rigid atoms, others: [32, 33, 34, 6, 8, 9, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35]) total number of confs: 638 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045818 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045818 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045818/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045818 Building REAL250005045819 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045819' /scratch/stefan/7916127/working/building/REAL250005045819 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045819 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045819/0 /scratch/stefan/7916127/working/building/REAL250005045819 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/970 `/scratch/stefan/7916127/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1) `REAL250005045819.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045819 none NC1=NN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 182, 100, 100, 100, 36, 23, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 197, 197, 197, 197, 182, 182, 100, 36, 36, 23, 23, 4, 1, 197, 197] 197 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: 708 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045819 none NC1=NN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 9, 33, 33, 33, 86, 134, 197, 197, 197, 197, 197, 197, 197, 197, 1, 1, 2, 2, 9, 9, 33, 86, 86, 134, 134, 197, 197, 1, 1] 197 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 780 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045819 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045819 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045819/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045819 Building REAL250005045820 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045820' /scratch/stefan/7916127/working/building/REAL250005045820 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045820 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045820/0 /scratch/stefan/7916127/working/building/REAL250005045820 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/971 `/scratch/stefan/7916127/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCCC1O)C1=CC(=O)[N-]O1) `REAL250005045820.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045820 none O=C(NCCNC(=O)C1CCCCC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [11, 1, 11, 11, 39, 54, 124, 124, 124, 181, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 11, 39, 39, 54, 54, 124, 181, 181, 181, 181, 181, 181, 181, 181, 181, 181, 543, 1] 543 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: 1153 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045820 none O=C(NCCNC(=O)C1CCCCC1O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 543 conformations in input total number of sets (complete confs): 543 using faster count positions algorithm for large data unique positions, atoms: [173, 171, 94, 57, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 171, 181, 181, 181, 181, 181, 173, 94, 94, 57, 57, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 181] 543 rigid atoms, others: [32, 33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 38, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 690 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045820 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045820 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045820/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045820 Building REAL250005045821 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045821' /scratch/stefan/7916127/working/building/REAL250005045821 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045821 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045821/0 /scratch/stefan/7916127/working/building/REAL250005045821 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/972 `/scratch/stefan/7916127/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C=CN=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045821.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045821 none CN1C=CN=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 193, 88, 88, 88, 37, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 193, 193, 88, 37, 37, 23, 23, 6, 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: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045821 none CN1C=CN=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 27, 27, 27, 81, 110, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 7, 7, 27, 81, 81, 110, 110, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25] set([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]) total number of confs: 719 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045821 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045821 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045821/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045821 Building REAL250005045822 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045822' /scratch/stefan/7916127/working/building/REAL250005045822 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045822 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045822/0 /scratch/stefan/7916127/working/building/REAL250005045822 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/973 `/scratch/stefan/7916127/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C) `REAL250005045822.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045822 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 4, 1, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 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: REAL250005045822 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 3, 7, 10, 11, 11, 11, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 7, 7, 10, 10, 11, 14, 1, 1, 1, 1, 2, 2, 2] 14 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 34, 17, 18, 19, 20, 21, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 62 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045822 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045822/1 /scratch/stefan/7916127/working/building/REAL250005045822 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/974 `/scratch/stefan/7916127/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C) `REAL250005045822.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045822/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045822 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 37, 37, 37, 20, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 37, 20, 20, 19, 19, 8, 1, 42, 42, 42, 42, 42, 42, 42] 42 rigid atoms, others: [33, 9, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 144 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: REAL250005045822 none CC1C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC[N@H+]1C 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', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 9, 6, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 10, 10, 10, 22, 26, 28, 28, 28, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 22, 22, 26, 26, 28, 42, 1, 1, 1, 1, 2, 2, 2] 42 rigid atoms, others: [0, 1, 2, 3, 36, 37, 35, 34, 17, 18, 19, 20, 21, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 149 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045822 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045822 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045822/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045822/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045822 Building REAL250005045823 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045823' /scratch/stefan/7916127/working/building/REAL250005045823 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045823 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045823/0 /scratch/stefan/7916127/working/building/REAL250005045823 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/975 `/scratch/stefan/7916127/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045823.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045823 none O=C(NCCNC(=O)C1=CN=CC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 37, 91, 91, 91, 147, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 9, 28, 28, 37, 37, 91, 147, 147, 147, 1] 147 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 372 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: REAL250005045823 none O=C(NCCNC(=O)C1=CN=CC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [143, 143, 83, 54, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 143, 147, 147, 147, 147, 147, 143, 83, 83, 54, 54, 10, 1, 1, 1, 147] 147 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30]) total number of confs: 547 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045823 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045823 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045823/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045823 Building REAL250005045824 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045824' /scratch/stefan/7916127/working/building/REAL250005045824 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045824 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045824/0 /scratch/stefan/7916127/working/building/REAL250005045824 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/976 `/scratch/stefan/7916127/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CNC(=O)S1)C1=CC(=O)[N-]O1) `REAL250005045824.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045824 none O=C(NCCNC(=O)C1=CNC(=O)S1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 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: [9, 1, 9, 9, 30, 39, 89, 89, 89, 118, 118, 118, 118, 118, 1, 1, 1, 1, 1, 1, 9, 30, 30, 39, 39, 89, 118, 118, 1] 118 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 362 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045824 none O=C(NCCNC(=O)C1=CNC(=O)S1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 11, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 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: [112, 112, 63, 49, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 112, 118, 118, 118, 118, 118, 112, 64, 64, 48, 48, 13, 1, 1, 118] 118 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28]) total number of confs: 417 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045824 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045824 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045824/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045824 Building REAL250005045825 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045825' /scratch/stefan/7916127/working/building/REAL250005045825 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045825 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045825/0 /scratch/stefan/7916127/working/building/REAL250005045825 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/977 `/scratch/stefan/7916127/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045825.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045825 none NC(=O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 171, 201, 153, 90, 90, 90, 31, 20, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 171, 171, 153, 153, 90, 31, 31, 20, 20, 6, 1] 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]) total number of confs: 770 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045825 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045825 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045825/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045825 Building REAL250005045826 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045826' /scratch/stefan/7916127/working/building/REAL250005045826 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045826 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045826/0 /scratch/stefan/7916127/working/building/REAL250005045826 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/978 `/scratch/stefan/7916127/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1) `REAL250005045826.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045826 none C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 171, 78, 78, 78, 32, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 171, 171, 201, 201, 201, 201, 201, 78, 32, 32, 19, 19, 4, 1, 171, 171, 171, 171] 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: 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: REAL250005045826 none C=CCC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CC1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', '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', '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, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 5, 1, 1, 1, 7, 7, 7, 42, 59, 157, 157, 157, 171, 171, 171, 171, 171, 1, 1, 17, 17, 17, 5, 5, 7, 42, 42, 59, 59, 157, 171, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 3, 4, 35, 34, 18, 19] set([0, 1, 5, 6, 7, 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: 577 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045826 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045826 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045826/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045826 Building REAL250005045827 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045827' /scratch/stefan/7916127/working/building/REAL250005045827 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045827 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045827/0 /scratch/stefan/7916127/working/building/REAL250005045827 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/979 `/scratch/stefan/7916127/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045827.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045827 none O=C(COC(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens 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, 142, 194, 201, 201, 21, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 142, 142, 201, 61, 21, 21, 12, 12, 4, 1] 201 rigid atoms, others: [11, 13, 14, 15, 16, 17, 18, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 703 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045827 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045827 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045827/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045827 Building REAL250005045828 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045828' /scratch/stefan/7916127/working/building/REAL250005045828 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045828 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045828/0 /scratch/stefan/7916127/working/building/REAL250005045828 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/980 `/scratch/stefan/7916127/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1) `REAL250005045828.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045828 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1 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.2', 'O.2', 'N.am', '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, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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, 129, 129, 129, 52, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 183, 183, 183, 183, 183, 183, 183, 183, 129, 52, 52, 36, 36, 11, 1, 183, 183, 183, 183, 183] 183 rigid atoms, others: [8, 10, 11, 12, 13, 14, 15, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35]) total number of confs: 595 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045828 none CC1(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC(=O)N1 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.2', 'O.2', 'N.am', '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, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 6, 4, 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: [1, 1, 1, 11, 11, 11, 50, 85, 169, 170, 169, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 2, 2, 2, 11, 50, 50, 85, 85, 170, 183, 1, 1, 1, 1, 1] 183 rigid atoms, others: [0, 1, 2, 35, 33, 32, 34, 16, 17, 18, 19, 20, 31] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 646 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045828 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045828 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045828/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045828 Building REAL250005045829 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045829' /scratch/stefan/7916127/working/building/REAL250005045829 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045829 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045829/0 /scratch/stefan/7916127/working/building/REAL250005045829 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/981 `/scratch/stefan/7916127/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CCCS1)C1=CC(=O)[N-]O1) `REAL250005045829.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045829 none O=C(NCCNC(=O)C1=CCCS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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, 5, 8, 1, 11, 1, 1, 5, 5, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 44, 101, 101, 101, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 9, 31, 31, 44, 44, 101, 132, 132, 132, 132, 132, 1] 132 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) 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: REAL250005045829 none O=C(NCCNC(=O)C1=CCCS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'S.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, 5, 8, 1, 11, 1, 1, 5, 5, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 70, 46, 11, 11, 1, 11, 1, 1, 1, 1, 1, 127, 132, 132, 132, 132, 132, 127, 71, 71, 46, 46, 11, 1, 1, 1, 1, 1, 132] 132 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30]) total number of confs: 496 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045829 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045829 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045829/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045829 Building REAL250005045830 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045830' /scratch/stefan/7916127/working/building/REAL250005045830 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045830 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045830/0 /scratch/stefan/7916127/working/building/REAL250005045830 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/982 `/scratch/stefan/7916127/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045830.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045830 none CC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 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: [154, 154, 154, 154, 108, 108, 108, 50, 34, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 154, 154, 154, 154, 154, 108, 50, 50, 34, 34, 9, 1, 154, 154] 154 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]) total number of confs: 518 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045830 none CC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 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] 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: [1, 1, 1, 1, 1, 1, 11, 11, 11, 56, 93, 144, 145, 145, 154, 154, 154, 154, 154, 1, 1, 1, 1, 1, 11, 56, 56, 93, 93, 145, 154, 1, 1] 154 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 19, 20, 21, 22, 23, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 596 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045830 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045830 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045830/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045830 Building REAL250005045831 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045831' /scratch/stefan/7916127/working/building/REAL250005045831 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045831 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045831/0 /scratch/stefan/7916127/working/building/REAL250005045831 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/983 `/scratch/stefan/7916127/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)NC1CC1) `REAL250005045831.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045831 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 8, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 24, 24, 89, 126, 200, 200, 200, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1, 1, 27, 89, 89, 126, 126, 200, 201, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 769 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045831 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C(=O)NC1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 11, 8, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 41, 24, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 118, 151, 151, 151, 201, 201, 118, 41, 41, 24, 24, 6, 1, 151, 201, 201, 201, 201, 201] 201 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: 693 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045831 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045831 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045831/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045831 Building REAL250005045832 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045832' /scratch/stefan/7916127/working/building/REAL250005045832 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045832 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045832/0 /scratch/stefan/7916127/working/building/REAL250005045832 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/984 `/scratch/stefan/7916127/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045832.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045832 none CCC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 155, 155, 155, 155, 85, 85, 85, 28, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 155, 85, 28, 28, 17, 17, 5, 1, 155, 155] 201 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: 762 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045832 none CCC1=NOC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 1, 1, 1, 1, 1, 1, 11, 11, 11, 48, 74, 145, 146, 145, 155, 155, 155, 155, 155, 1, 12, 13, 13, 12, 12, 1, 11, 48, 48, 74, 74, 146, 155, 1, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 34, 35, 20, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 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/7916127/working/building/REAL250005045832 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045832 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045832/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045832 Building REAL250005045833 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045833' /scratch/stefan/7916127/working/building/REAL250005045833 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045833 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045833/0 /scratch/stefan/7916127/working/building/REAL250005045833 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/985 `/scratch/stefan/7916127/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045833.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045833 none NC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 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 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, 71, 71, 71, 33, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 71, 33, 33, 24, 24, 11, 1, 87] 87 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]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045833 none NC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'N.pl3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 6, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 6, 4, 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 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, 8, 8, 8, 31, 48, 79, 79, 79, 87, 87, 87, 87, 87, 1, 1, 1, 1, 8, 31, 31, 48, 48, 79, 87, 1] 87 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 22, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 317 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045833 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045833 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045833/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045833 Building REAL250005045834 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045834' /scratch/stefan/7916127/working/building/REAL250005045834 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045834 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045834/0 /scratch/stefan/7916127/working/building/REAL250005045834 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/986 `/scratch/stefan/7916127/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCSC1)C1=CC(=O)[N-]O1) `REAL250005045834.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045834 none O=C(NCCNC(=O)C1CCSC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [9, 1, 9, 9, 30, 42, 94, 94, 94, 154, 154, 154, 154, 1, 1, 1, 1, 1, 1, 9, 30, 30, 42, 42, 94, 154, 154, 154, 154, 154, 154, 154, 1] 154 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 494 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: REAL250005045834 none O=C(NCCNC(=O)C1CCSC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'S.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 5, 14, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [149, 149, 88, 53, 10, 10, 1, 10, 1, 1, 1, 1, 1, 149, 154, 154, 154, 154, 154, 149, 88, 88, 53, 53, 10, 1, 1, 1, 1, 1, 1, 1, 154] 154 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 576 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045834 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045834 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045834/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045834 Building REAL250005045835 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045835' /scratch/stefan/7916127/working/building/REAL250005045835 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045835 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045835/0 /scratch/stefan/7916127/working/building/REAL250005045835 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/987 `/scratch/stefan/7916127/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCO1)C1=CC(=O)[N-]O1) `REAL250005045835.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045835 none O=C(NCCNC(=O)C1CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 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: [7, 1, 7, 7, 23, 34, 78, 78, 78, 107, 107, 107, 1, 1, 1, 1, 1, 1, 7, 23, 23, 34, 34, 78, 107, 107, 107, 107, 107, 1] 107 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) 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: REAL250005045835 none O=C(NCCNC(=O)C1CCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', '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, 5, 8, 1, 11, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 106, 70, 56, 12, 12, 1, 12, 1, 1, 1, 1, 106, 107, 107, 107, 107, 107, 107, 70, 70, 56, 56, 12, 1, 1, 1, 1, 1, 107] 107 rigid atoms, others: [6, 8, 9, 10, 11, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29]) total number of confs: 408 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045835 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045835 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045835/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045835 Building REAL250005045836 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045836' /scratch/stefan/7916127/working/building/REAL250005045836 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045836 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045836/0 /scratch/stefan/7916127/working/building/REAL250005045836 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/988 `/scratch/stefan/7916127/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045836.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045836 none CCCC(O)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 148, 103, 148, 51, 51, 51, 18, 11, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 148, 444, 103, 103, 51, 18, 18, 11, 11, 3, 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: 1362 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045836 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045836 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045836/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045836 Building REAL250005045837 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045837' /scratch/stefan/7916127/working/building/REAL250005045837 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045837 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045837/0 /scratch/stefan/7916127/working/building/REAL250005045837 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/989 `/scratch/stefan/7916127/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC#N)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045837.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045837 none CC(C)(CC#N)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [159, 81, 159, 157, 199, 199, 81, 81, 31, 22, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 159, 201, 201, 81, 31, 31, 22, 22, 6, 1] 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]) total number of confs: 888 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045837 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045837 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045837/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045837 Building REAL250005045838 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045838' /scratch/stefan/7916127/working/building/REAL250005045838 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045838 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045838/0 /scratch/stefan/7916127/working/building/REAL250005045838 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/990 `/scratch/stefan/7916127/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(Cl)CC1)C1=CC(=O)[N-]O1) `REAL250005045838.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045838 none O=C(NCCNC(=O)C1(Cl)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 32, 43, 114, 114, 114, 176, 176, 176, 1, 1, 1, 1, 1, 1, 9, 32, 32, 43, 43, 114, 176, 176, 176, 176, 1] 176 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 574 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: REAL250005045838 none O=C(NCCNC(=O)C1(Cl)CC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'Cl', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 16, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 104, 70, 13, 13, 1, 13, 1, 1, 1, 1, 169, 176, 176, 176, 176, 176, 169, 104, 104, 70, 70, 13, 1, 1, 1, 1, 176] 176 rigid atoms, others: [6, 8, 9, 10, 11, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28]) total number of confs: 662 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045838 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045838 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045838/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045838 Building REAL250005045839 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045839' /scratch/stefan/7916127/working/building/REAL250005045839 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045839 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045839/0 /scratch/stefan/7916127/working/building/REAL250005045839 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/991 `/scratch/stefan/7916127/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCCO1) `REAL250005045839.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045839 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 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: [8, 1, 8, 8, 34, 46, 75, 75, 75, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 8, 33, 33, 46, 46, 75, 82, 1, 1, 1, 1, 1] 82 rigid atoms, others: [1, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25]) 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: REAL250005045839 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', '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, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 5, 5, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 3, 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: [75, 75, 40, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 75, 82, 82, 82, 82, 75, 40, 40, 27, 27, 9, 1, 82, 82, 82, 82, 82] 82 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 25] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30]) total number of confs: 278 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045839 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045839 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045839/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045839 Building REAL250005045840 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045840' /scratch/stefan/7916127/working/building/REAL250005045840 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045840 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045840/0 /scratch/stefan/7916127/working/building/REAL250005045840 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/992 `/scratch/stefan/7916127/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(CO)O1) `REAL250005045840.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045840 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(CO)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 5, 12, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 558 conformations in input total number of sets (complete confs): 558 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 8, 34, 56, 148, 148, 148, 173, 173, 173, 173, 173, 1, 1, 1, 1, 1, 8, 1, 9, 34, 34, 56, 56, 148, 173, 1, 1, 8, 8, 24] 558 rigid atoms, others: [1, 14, 15, 16, 17, 18, 20, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32]) total number of confs: 571 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045840 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=CC=C(CO)O1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 1, 1, 5, 12, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 4, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 558 conformations in input total number of sets (complete confs): 558 using faster count positions algorithm for large data unique positions, atoms: [143, 142, 49, 27, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 142, 173, 173, 173, 173, 186, 173, 143, 49, 49, 27, 27, 7, 1, 173, 173, 186, 186, 558] 558 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]) total number of confs: 1145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045840 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045840 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045840/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045840 Building REAL250005045841 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045841' /scratch/stefan/7916127/working/building/REAL250005045841 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045841 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045841/0 /scratch/stefan/7916127/working/building/REAL250005045841 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/993 `/scratch/stefan/7916127/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CO)COC1)C1=CC(=O)[N-]O1) `REAL250005045841.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045841 none O=C(NCCNC(=O)C1(CO)COC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 3, 7, 3, 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: [8, 1, 8, 8, 24, 35, 103, 103, 103, 176, 201, 176, 176, 176, 1, 1, 1, 1, 1, 1, 8, 24, 24, 35, 35, 103, 201, 201, 603, 176, 176, 176, 176, 1] 603 rigid atoms, others: [1, 33, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 1304 number of broken/clashed sets: 158 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045841 none O=C(NCCNC(=O)C1(CO)COC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [159, 158, 67, 43, 7, 7, 1, 7, 1, 1, 6, 1, 1, 1, 158, 176, 176, 176, 176, 176, 159, 67, 67, 43, 43, 7, 6, 6, 18, 1, 1, 1, 1, 176] 603 rigid atoms, others: [32, 6, 8, 9, 11, 12, 13, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33]) total number of confs: 619 number of broken/clashed sets: 158 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045841 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045841 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045841/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045841 Building REAL250005045842 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045842' /scratch/stefan/7916127/working/building/REAL250005045842 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045842 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045842/0 /scratch/stefan/7916127/working/building/REAL250005045842 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/994 `/scratch/stefan/7916127/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC(C#N)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045842.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045842 none CC1CC(C#N)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 121, 201, 201, 121, 121, 34, 22, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 121, 34, 34, 22, 22, 6, 1, 201, 201] 201 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: 620 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: REAL250005045842 none CC1CC(C#N)(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 8, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 42, 75, 197, 197, 197, 201, 201, 201, 201, 201, 1, 2, 2, 2, 1, 1, 1, 6, 42, 42, 75, 75, 197, 201, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 34, 35, 20, 24, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 676 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045842 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045842 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045842/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045842 Building REAL250005045843 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045843' /scratch/stefan/7916127/working/building/REAL250005045843 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045843 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045843/0 /scratch/stefan/7916127/working/building/REAL250005045843 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/995 `/scratch/stefan/7916127/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)=CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045843.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045843 none CC(C)=CCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 5, 1, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 178, 158, 64, 64, 64, 36, 21, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 179, 179, 159, 159, 64, 36, 36, 21, 21, 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: 859 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045843 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045843 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045843/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045843 Building REAL250005045844 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045844' /scratch/stefan/7916127/working/building/REAL250005045844 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045844 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045844/0 /scratch/stefan/7916127/working/building/REAL250005045844 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/996 `/scratch/stefan/7916127/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=C(C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)CC) `REAL250005045844.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045844 none CC=C(C=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1)CC NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 70, 70, 44, 44, 44, 20, 13, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 128, 201, 128, 128, 128, 128, 70, 70, 44, 20, 20, 13, 13, 4, 1, 201, 201, 201, 201, 201] 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: 874 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045844 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045844 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045844/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045844 Building REAL250005045845 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045845' /scratch/stefan/7916127/working/building/REAL250005045845 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045845 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045845/0 /scratch/stefan/7916127/working/building/REAL250005045845 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/997 `/scratch/stefan/7916127/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1COC1)C1=CC(=O)[N-]O1) `REAL250005045845.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045845 none O=C(NCCNC(=O)C1COC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 38, 60, 124, 124, 124, 201, 201, 201, 1, 1, 1, 1, 1, 1, 9, 38, 38, 60, 60, 124, 201, 201, 201, 201, 201, 1] 201 rigid atoms, others: [1, 12, 13, 14, 15, 16, 17, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 679 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: REAL250005045845 none O=C(NCCNC(=O)C1COC1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 108, 63, 13, 13, 1, 13, 1, 1, 1, 1, 189, 201, 201, 201, 201, 201, 189, 108, 108, 63, 63, 13, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [6, 8, 9, 10, 11, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29]) total number of confs: 722 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045845 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045845 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045845/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045845 Building REAL250005045846 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045846' /scratch/stefan/7916127/working/building/REAL250005045846 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045846 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045846/0 /scratch/stefan/7916127/working/building/REAL250005045846 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/998 `/scratch/stefan/7916127/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045846.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045846 none O=C(C=CC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 173, 173, 201, 201, 201, 201, 32, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 173, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 32, 32, 23, 23, 6, 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: 617 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045846 none O=C(C=CC1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 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, 6, 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, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 8, 8, 1, 1, 1, 1, 1, 1, 36, 36, 99, 130, 201, 201, 201, 201, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 99, 99, 130, 130, 201, 201] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 765 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045846 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045846 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045846/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045846 Building REAL250005045847 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045847' /scratch/stefan/7916127/working/building/REAL250005045847 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045847 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045847/0 /scratch/stefan/7916127/working/building/REAL250005045847 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/999 `/scratch/stefan/7916127/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1CCC(=O)C1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045847.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045847 none O=C(CC1CCC(=O)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 1, 11, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 169, 201, 201, 201, 201, 201, 28, 19, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 170, 170, 201, 201, 201, 201, 201, 201, 201, 50, 28, 28, 19, 19, 4, 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: 768 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045847 none O=C(CC1CCC(=O)C1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', '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: [11, 1, 5, 5, 5, 5, 1, 11, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens 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, 7, 1, 1, 1, 1, 1, 1, 1, 32, 32, 110, 130, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 32, 110, 110, 130, 130, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045847 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045847 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045847/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045847 Building REAL250005045848 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045848' /scratch/stefan/7916127/working/building/REAL250005045848 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045848 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045848/0 /scratch/stefan/7916127/working/building/REAL250005045848 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1000 `/scratch/stefan/7916127/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1) `REAL250005045848.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045848 none N#CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 127, 127, 127, 48, 36, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 201, 201, 201, 127, 48, 48, 36, 36, 12, 1, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [10, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33]) total number of confs: 534 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045848 none N#CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCC1 NO_LONG_NAME dock atom types: ['N.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 5, 5, 5, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 72, 107, 183, 183, 183, 201, 201, 201, 201, 201, 1, 1, 1, 12, 72, 72, 107, 107, 183, 201, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 18, 19, 20, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 708 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045848 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045848 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045848/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045848 Building REAL250005045849 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045849' /scratch/stefan/7916127/working/building/REAL250005045849 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045849 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045849/0 /scratch/stefan/7916127/working/building/REAL250005045849 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1001 `/scratch/stefan/7916127/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1) `REAL250005045849.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045849 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 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: [168, 167, 168, 167, 122, 122, 123, 51, 32, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 167, 168, 168, 168, 167, 168, 168, 167, 168, 167, 123, 51, 51, 32, 32, 9, 1] 168 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]) total number of confs: 559 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045849 none CC1CCC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 12, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 59, 98, 159, 160, 159, 168, 168, 168, 168, 167, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 59, 59, 98, 98, 160, 168] 168 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23, 24, 25, 26, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 647 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045849 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045849 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045849/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045849 Building REAL250005045850 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045850' /scratch/stefan/7916127/working/building/REAL250005045850 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045850 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045850/0 /scratch/stefan/7916127/working/building/REAL250005045850 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1002 `/scratch/stefan/7916127/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=CNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045850.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045850 none NC1=CNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 6, 4, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 72, 34, 23, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 72, 72, 72, 71, 72, 34, 34, 23, 23, 7, 1] 72 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]) 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: REAL250005045850 none NC1=CNN=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 7, 4, 7, 7, 7, 6, 4, 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 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, 1, 3, 3, 3, 19, 34, 70, 70, 70, 72, 72, 72, 72, 72, 1, 1, 1, 1, 3, 19, 19, 34, 34, 70, 72] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045850 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045850/1 /scratch/stefan/7916127/working/building/REAL250005045850 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1003 `/scratch/stefan/7916127/working/3D/1003' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NN=C1) `REAL250005045850.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045850/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045850 none NC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NN=C1 NO_LONG_NAME dock atom types: ['N.pl3', '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', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 1, 6, 6, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 118, 118, 118, 51, 35, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 167, 167, 167, 167, 167, 118, 51, 51, 35, 35, 11, 1, 167, 167] 167 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]) total number of confs: 474 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045850 none NC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)NN=C1 NO_LONG_NAME dock atom types: ['N.pl3', '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', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 8, 1, 6, 6, 6, 7, 7, 7, 7, 6, 7, 6, 7] dock color type numbers: [4, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 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: [1, 1, 1, 1, 11, 11, 11, 54, 88, 157, 157, 157, 167, 167, 167, 167, 167, 1, 1, 1, 1, 1, 11, 54, 54, 88, 88, 157, 167, 1, 1] 167 rigid atoms, others: [0, 1, 2, 3, 17, 18, 19, 20, 21, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 598 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045850 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045850 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045850/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045850/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045850 Building REAL250005045851 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045851' /scratch/stefan/7916127/working/building/REAL250005045851 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045851 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045851/0 /scratch/stefan/7916127/working/building/REAL250005045851 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1004 `/scratch/stefan/7916127/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C=CCO)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045851.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045851 none O=C(C=CCO)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 1, 1, 5, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 4, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [113, 113, 113, 177, 177, 201, 49, 35, 8, 9, 1, 9, 1, 1, 1, 1, 1, 1, 177, 177, 201, 201, 603, 113, 49, 49, 35, 35, 9, 1] 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]) total number of confs: 1354 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045851 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045851 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045851/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045851 Building REAL250005045852 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045852' /scratch/stefan/7916127/working/building/REAL250005045852 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045852 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045852/0 /scratch/stefan/7916127/working/building/REAL250005045852 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1005 `/scratch/stefan/7916127/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1(CO)CCCO1)C1=CC(=O)[N-]O1) `REAL250005045852.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045852 none O=C(NCCNC(=O)C1(CO)CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 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, 6, 24, 36, 99, 99, 99, 191, 201, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 6, 24, 24, 36, 36, 99, 201, 201, 603, 191, 191, 191, 191, 191, 191, 1] 603 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: 1257 number of broken/clashed sets: 174 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045852 none O=C(NCCNC(=O)C1(CO)CCCO1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 5, 12, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 7, 7, 3, 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: [185, 184, 81, 57, 11, 11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 184, 191, 191, 191, 191, 191, 185, 81, 81, 57, 57, 11, 8, 8, 24, 1, 1, 1, 1, 1, 1, 191] 603 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36]) total number of confs: 692 number of broken/clashed sets: 174 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045852 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045852 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045852/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045852 Building REAL250005045853 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045853' /scratch/stefan/7916127/working/building/REAL250005045853 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045853 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045853/0 /scratch/stefan/7916127/working/building/REAL250005045853 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1006 `/scratch/stefan/7916127/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045853.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045853 none CCC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 136, 136, 136, 136, 136, 79, 79, 79, 34, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 136, 136, 136, 79, 34, 34, 20, 20, 4, 1] 201 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: 750 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: REAL250005045853 none CCC1=CNC=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 48, 71, 130, 130, 130, 136, 136, 136, 136, 136, 6, 6, 6, 6, 6, 1, 1, 1, 10, 48, 48, 71, 71, 130, 136] 201 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 504 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045853 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045853 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045853/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045853 Building REAL250005045854 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045854' /scratch/stefan/7916127/working/building/REAL250005045854 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045854 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045854/0 /scratch/stefan/7916127/working/building/REAL250005045854 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1007 `/scratch/stefan/7916127/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CCC[C@H]1CF)C1=CC(=O)[N-]O1) `REAL250005045854.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045854 none O=C(NCCNC(=O)[C@@H]1CCC[C@H]1CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens 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, 18, 30, 89, 89, 89, 196, 196, 196, 196, 196, 196, 196, 201, 1, 1, 1, 1, 1, 1, 4, 18, 18, 30, 30, 89, 196, 196, 196, 196, 196, 196, 201, 201, 1] 201 rigid atoms, others: [1, 37, 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]) total number of confs: 626 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: REAL250005045854 none O=C(NCCNC(=O)[C@@H]1CCC[C@H]1CF)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'C.2', 'C.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, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 7, 5, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [182, 180, 71, 50, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 7, 180, 196, 196, 196, 196, 196, 182, 71, 71, 50, 50, 10, 1, 1, 1, 1, 1, 1, 7, 7, 196] 201 rigid atoms, others: [32, 33, 34, 6, 8, 9, 10, 11, 12, 13, 14, 15, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37]) total number of confs: 658 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045854 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045854 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045854/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045854 Building REAL250005045855 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045855' /scratch/stefan/7916127/working/building/REAL250005045855 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045855 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045855/0 /scratch/stefan/7916127/working/building/REAL250005045855 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1008 `/scratch/stefan/7916127/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](O)[C@@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045855.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045855 none CC(C)[C@@H](O)[C@@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', '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', 'H', '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, 7, 12, 5, 7, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 6, 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 258 conformations in input total number of sets (complete confs): 258 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 81, 86, 86, 50, 81, 81, 50, 50, 21, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 258, 81, 81, 81, 50, 21, 21, 14, 14, 4, 1] 258 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: 599 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045855 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045855 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045855/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045855 Building REAL250005045856 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045856' /scratch/stefan/7916127/working/building/REAL250005045856 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045856 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045856/0 /scratch/stefan/7916127/working/building/REAL250005045856 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1009 `/scratch/stefan/7916127/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=CN1CCCC1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045856.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045856 none O=CN1CCCC1C(=O)NCCNC(=O)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', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 189, 112, 112, 112, 42, 27, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 189, 189, 189, 189, 189, 189, 189, 189, 112, 42, 42, 27, 27, 9, 1] 189 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: 607 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045856 none O=CN1CCCC1C(=O)NCCNC(=O)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', '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', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 55, 87, 173, 173, 173, 189, 189, 189, 189, 189, 2, 1, 1, 1, 1, 1, 1, 1, 10, 55, 55, 87, 87, 173, 189] 189 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 653 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045856 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045856 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045856/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045856 Building REAL250005045857 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045857' /scratch/stefan/7916127/working/building/REAL250005045857 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045857 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045857/0 /scratch/stefan/7916127/working/building/REAL250005045857 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1010 `/scratch/stefan/7916127/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1) `REAL250005045857.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045857 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 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 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 66, 66, 34, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 34, 34, 22, 22, 9, 1] 66 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]) 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: REAL250005045857 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 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 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, 4, 4, 4, 22, 33, 62, 62, 62, 66, 66, 66, 66, 66, 1, 2, 2, 2, 1, 4, 22, 22, 33, 33, 62, 66] 66 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 23] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045857 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045857/1 /scratch/stefan/7916127/working/building/REAL250005045857 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1011 `/scratch/stefan/7916127/working/3D/1011' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1) `REAL250005045857.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045857 none CC1=NN=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 82, 82, 47, 28, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 47, 47, 28, 28, 11, 1, 82] 82 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]) 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: REAL250005045857 none CC1=NN=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.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', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 24, 37, 74, 74, 74, 82, 82, 82, 82, 82, 1, 2, 2, 2, 4, 24, 24, 37, 37, 74, 82, 1] 82 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 280 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045857 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045857 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045857/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045857/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045857 Building REAL250005045858 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045858' /scratch/stefan/7916127/working/building/REAL250005045858 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045858 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045858/0 /scratch/stefan/7916127/working/building/REAL250005045858 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1012 `/scratch/stefan/7916127/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CN=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045858.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045858 none CC1=CN=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 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] 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, 104, 102, 102, 102, 56, 37, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 104, 104, 104, 104, 104, 102, 56, 56, 37, 37, 7, 1, 104] 104 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]) total number of confs: 365 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045858 none CC1=CN=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'N.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 3, 3, 7, 7, 6, 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] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 29, 47, 100, 100, 100, 104, 104, 104, 104, 104, 1, 2, 2, 2, 1, 7, 29, 29, 47, 47, 100, 104, 1] 104 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 20, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 359 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045858 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045858 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045858/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045858 Building REAL250005045859 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045859' /scratch/stefan/7916127/working/building/REAL250005045859 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045859 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045859/0 /scratch/stefan/7916127/working/building/REAL250005045859 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1013 `/scratch/stefan/7916127/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1C[C@@H]1C(F)F)C1=CC(=O)[N-]O1) `REAL250005045859.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045859 none O=C(NCCNC(=O)[C@@H]1C[C@@H]1C(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 3, 21, 32, 89, 89, 89, 165, 165, 165, 165, 165, 201, 201, 1, 1, 1, 1, 1, 1, 3, 20, 20, 32, 32, 89, 165, 165, 201, 1] 201 rigid atoms, others: [1, 16, 17, 18, 19, 20, 21, 31] 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]) total number of confs: 732 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045859 none O=C(NCCNC(=O)[C@@H]1C[C@@H]1C(F)F)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 71, 50, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 158, 165, 165, 165, 165, 165, 158, 71, 71, 50, 50, 10, 1, 1, 6, 165] 201 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31]) total number of confs: 573 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045859 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045859 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045859/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045859 Building REAL250005045860 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045860' /scratch/stefan/7916127/working/building/REAL250005045860 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045860 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045860/0 /scratch/stefan/7916127/working/building/REAL250005045860 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1014 `/scratch/stefan/7916127/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(=O)N1) `REAL250005045860.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045860 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 6, 4, 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: [10, 1, 10, 10, 42, 62, 105, 105, 105, 113, 113, 113, 113, 113, 1, 1, 1, 1, 1, 1, 10, 42, 42, 62, 62, 105, 113, 1, 1] 113 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045860 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(=O)N1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7, 6] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 6, 4, 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: [71, 71, 31, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 71, 113, 113, 113, 113, 113, 71, 31, 31, 22, 22, 9, 1, 113, 113] 113 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]) total number of confs: 308 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045860 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045860/1 /scratch/stefan/7916127/working/building/REAL250005045860 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1015 `/scratch/stefan/7916127/working/3D/1015' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(=O)[N-]1) `REAL250005045860.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045860/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045860 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 14, 17, 27, 27, 27, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 3, 13, 13, 17, 17, 27, 31, 1] 31 rigid atoms, others: [1, 14, 15, 16, 17, 18, 19, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045860 none O=C(NCCNC(=O)C1=CC(=O)[N-]O1)C1=COC(=O)[N-]1 NO_LONG_NAME dock atom types: ['O.2', 'C.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.2', 'C.2', 'O.3', 'C.2', 'O.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 1, 12, 1, 11, 8, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 3, 7, 5, 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, 16, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 16, 16, 12, 12, 7, 1, 31] 31 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]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045860 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045860 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045860/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045860/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045860 Building REAL250005045861 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045861' /scratch/stefan/7916127/working/building/REAL250005045861 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045861 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045861/0 /scratch/stefan/7916127/working/building/REAL250005045861 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1016 `/scratch/stefan/7916127/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045861.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045861 none CC=CC(O)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 12, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 155, 108, 155, 108, 108, 39, 23, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 155, 465, 108, 39, 39, 23, 23, 5, 1] 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]) total number of confs: 1238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045861 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045861 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045861/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045861 Building REAL250005045862 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045862' /scratch/stefan/7916127/working/building/REAL250005045862 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045862 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045862/0 /scratch/stefan/7916127/working/building/REAL250005045862 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1017 `/scratch/stefan/7916127/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC[C@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045862.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045862 none CCCC[C@H](C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', '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, 7, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7] 0 hydrogens 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, 181, 173, 127, 44, 127, 127, 44, 44, 25, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 181, 181, 176, 176, 127, 127, 127, 44, 25, 25, 16, 16, 4, 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: 974 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045862 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045862 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045862/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045862 Building REAL250005045863 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045863' /scratch/stefan/7916127/working/building/REAL250005045863 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL250005045863 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045863/0 /scratch/stefan/7916127/working/building/REAL250005045863 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1018 `/scratch/stefan/7916127/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C) `REAL250005045863.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045863 none C[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)[NH+](C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.4', 'H', '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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 9, 6, 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, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 14, 14, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 14, 14, 9, 1, 21, 21, 21, 21, 21, 21] 21 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: 74 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045863 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045863/1 /scratch/stefan/7916127/working/building/REAL250005045863 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1019 `/scratch/stefan/7916127/working/3D/1019' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N(C)C) `REAL250005045863.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045863/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005045863 none C[C@@H](C(=O)NCCNC(=O)C1=CC(=O)[N-]O1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', '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', 'N.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, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 10, 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, 7, 6, 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, 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: [164, 109, 164, 109, 109, 46, 31, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 164, 170, 170, 164, 164, 164, 109, 46, 46, 31, 31, 9, 1, 170, 170, 170, 170, 170, 170] 170 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]) total number of confs: 635 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045863 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045863 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045863/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045863/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045863 Building REAL250005045864 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045864' /scratch/stefan/7916127/working/building/REAL250005045864 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045864 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045864/0 /scratch/stefan/7916127/working/building/REAL250005045864 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1020 `/scratch/stefan/7916127/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045864.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045864 none CCC=C(F)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 15, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 135, 135, 92, 135, 92, 92, 38, 23, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 199, 201, 201, 201, 201, 135, 92, 38, 38, 23, 23, 6, 1] 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]) total number of confs: 830 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045864 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045864 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045864/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045864 Building REAL250005045865 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045865' /scratch/stefan/7916127/working/building/REAL250005045865 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045865 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045865/0 /scratch/stefan/7916127/working/building/REAL250005045865 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1021 `/scratch/stefan/7916127/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1C2(CC2)C12CC2)C1=CC(=O)[N-]O1) `REAL250005045865.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045865 none O=C(NCCNC(=O)C1C2(CC2)C12CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [4, 1, 4, 4, 18, 31, 91, 91, 91, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 4, 18, 18, 31, 31, 91, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 620 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: REAL250005045865 none O=C(NCCNC(=O)C1C2(CC2)C12CC2)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', '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, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 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: [201, 201, 94, 65, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 94, 94, 65, 65, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201] 201 rigid atoms, others: [32, 33, 34, 35, 6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36]) total number of confs: 707 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045865 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045865 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045865/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045865 Building REAL250005045866 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045866' /scratch/stefan/7916127/working/building/REAL250005045866 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045866 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045866/0 /scratch/stefan/7916127/working/building/REAL250005045866 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1022 `/scratch/stefan/7916127/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045866.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045866 none CCC=CC(=O)NCCNC(=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', 'N.am', 'C.2', 'O.2', 'C.2', '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, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 164, 164, 100, 100, 100, 44, 26, 5, 6, 1, 6, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 164, 164, 100, 44, 44, 26, 26, 6, 1] 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]) total number of confs: 773 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045866 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045866 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045866/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045866 Building REAL250005045867 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045867' /scratch/stefan/7916127/working/building/REAL250005045867 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045867 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045867/0 /scratch/stefan/7916127/working/building/REAL250005045867 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1023 `/scratch/stefan/7916127/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N) `REAL250005045867.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045867 none CN1N=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 87, 87, 87, 51, 35, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 89, 87, 51, 51, 35, 35, 7, 1, 89, 89] 89 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]) total number of confs: 305 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: REAL250005045867 none CN1N=NC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'N.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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 28, 43, 83, 83, 83, 89, 89, 89, 89, 89, 1, 1, 2, 2, 2, 5, 27, 27, 43, 43, 83, 89, 2, 2] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20] set([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]) total number of confs: 313 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045867 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045867 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045867/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045867 Building REAL250005045868 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045868' /scratch/stefan/7916127/working/building/REAL250005045868 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045868 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045868/0 /scratch/stefan/7916127/working/building/REAL250005045868 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1024 `/scratch/stefan/7916127/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(F)(F)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045868.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045868 none CCC(F)(F)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'F', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 15, 15, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 105 conformations in input total number of sets (complete confs): 105 using faster count positions algorithm for large data unique positions, atoms: [105, 101, 82, 101, 101, 69, 69, 69, 23, 18, 4, 5, 1, 5, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 83, 83, 69, 23, 23, 18, 18, 5, 1] 105 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]) total number of confs: 419 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045868 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045868 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045868/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045868 Building REAL250005045869 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045869' /scratch/stefan/7916127/working/building/REAL250005045869 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045869 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045869/0 /scratch/stefan/7916127/working/building/REAL250005045869 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1025 `/scratch/stefan/7916127/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NOC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045869.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045869 none CC1=NOC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 140, 48, 48, 48, 25, 16, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 140, 140, 48, 25, 25, 16, 16, 4, 1] 201 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]) total number of confs: 656 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045869 none CC1=NOC=C1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 1, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 41, 41, 41, 114, 124, 201, 201, 201, 201, 201, 201, 201, 201, 2, 2, 2, 1, 8, 8, 41, 114, 114, 124, 124, 201, 201] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 724 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045869 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045869 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045869/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045869 Building REAL250005045870 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045870' /scratch/stefan/7916127/working/building/REAL250005045870 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045870 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045870/0 /scratch/stefan/7916127/working/building/REAL250005045870 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1026 `/scratch/stefan/7916127/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=CSN=N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045870.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045870 none O=C(CC1=CSN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 165, 201, 201, 201, 201, 22, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 165, 165, 201, 68, 22, 22, 13, 13, 5, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045870 none O=C(CC1=CSN=N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'S.3', 'N.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 1, 1, 14, 8, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 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] 0 hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 33, 33, 117, 142, 200, 200, 200, 201, 201, 201, 201, 201, 5, 5, 1, 33, 117, 117, 142, 142, 200, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 788 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045870 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045870 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045870/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045870 Building REAL250005045871 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045871' /scratch/stefan/7916127/working/building/REAL250005045871 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045871 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045871/0 /scratch/stefan/7916127/working/building/REAL250005045871 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1027 `/scratch/stefan/7916127/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1) `REAL250005045871.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045871 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 96, 96, 96, 44, 29, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 137, 137, 137, 137, 137, 137, 137, 96, 44, 44, 29, 29, 10, 1, 137, 137, 137, 137, 137, 137, 137, 137] 137 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: 412 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045871 none CC1=C(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)CCCC1 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, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 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 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 31, 53, 122, 124, 124, 137, 137, 137, 137, 137, 1, 1, 1, 1, 2, 2, 2, 7, 31, 31, 53, 53, 124, 137, 1, 1, 1, 1, 1, 1, 1, 1] 137 rigid atoms, others: [0, 1, 2, 3, 36, 33, 35, 32, 34, 17, 18, 19, 20, 38, 37, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 460 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045871 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045871 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045871/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045871 Building REAL250005045872 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045872' /scratch/stefan/7916127/working/building/REAL250005045872 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045872 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045872/0 /scratch/stefan/7916127/working/building/REAL250005045872 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1028 `/scratch/stefan/7916127/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(C[C@H]1COC(=O)N1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045872.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045872 none O=C(C[C@H]1COC(=O)N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 12, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 6, 4, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 101, 101, 180, 201, 201, 201, 201, 201, 201, 35, 21, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 181, 181, 201, 201, 201, 101, 35, 35, 21, 21, 4, 1] 201 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: 778 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045872 none O=C(C[C@H]1COC(=O)N1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 5, 7, 5, 12, 1, 11, 8, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 7, 6, 4, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 89, 120, 201, 201, 201, 201, 201, 201, 201, 201, 7, 7, 1, 1, 1, 27, 89, 89, 120, 120, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 762 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045872 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045872 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045872/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045872 Building REAL250005045873 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045873' /scratch/stefan/7916127/working/building/REAL250005045873 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045873 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045873/0 /scratch/stefan/7916127/working/building/REAL250005045873 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1029 `/scratch/stefan/7916127/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1) `REAL250005045873.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045873 none CC(C)C1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 97, 97, 97, 37, 24, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 37, 37, 24, 24, 4, 1, 201, 201] 201 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: 632 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: REAL250005045873 none CC(C)C1CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 5, 5, 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, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 1, 13, 13, 13, 61, 90, 201, 201, 201, 201, 201, 201, 201, 201, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 13, 61, 61, 90, 90, 201, 201, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 20, 28, 29, 30, 31] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 709 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045873 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045873 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045873/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045873 Building REAL250005045874 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045874' /scratch/stefan/7916127/working/building/REAL250005045874 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045874 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045874/0 /scratch/stefan/7916127/working/building/REAL250005045874 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1030 `/scratch/stefan/7916127/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CCOC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045874.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045874 none CC1CCOC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 87, 87, 87, 35, 22, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 87, 35, 35, 22, 22, 5, 1] 118 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: 446 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: REAL250005045874 none CC1CCOC1CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 51, 69, 118, 118, 118, 118, 118, 118, 118, 118, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 12, 51, 51, 69, 69, 118, 118] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 437 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045874 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045874 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045874/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045874 Building REAL250005045875 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045875' /scratch/stefan/7916127/working/building/REAL250005045875 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045875 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045875/0 /scratch/stefan/7916127/working/building/REAL250005045875 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1031 `/scratch/stefan/7916127/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CNC(=O)C1)C1=CC(=O)[N-]O1) `REAL250005045875.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045875 none O=C(NCCNC(=O)C1CNC(=O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 31, 45, 110, 110, 110, 178, 178, 178, 178, 178, 1, 1, 1, 1, 1, 1, 9, 31, 31, 45, 45, 110, 178, 178, 178, 178, 178, 178, 1] 178 rigid atoms, others: [32, 1, 14, 15, 16, 17, 18, 19] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 574 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: REAL250005045875 none O=C(NCCNC(=O)C1CNC(=O)C1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 5, 5, 8, 1, 11, 5, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 178 conformations in input total number of sets (complete confs): 178 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 88, 54, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 169, 178, 178, 178, 178, 178, 169, 88, 88, 54, 54, 10, 1, 1, 1, 1, 1, 1, 178] 178 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]) total number of confs: 638 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045875 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045875 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045875/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045875 Building REAL250005045876 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045876' /scratch/stefan/7916127/working/building/REAL250005045876 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045876 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045876/0 /scratch/stefan/7916127/working/building/REAL250005045876 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1032 `/scratch/stefan/7916127/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=C1) `REAL250005045876.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045876 none NC1=CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 179, 104, 104, 104, 36, 20, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 179, 179, 104, 36, 36, 20, 20, 4, 1, 201] 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]) total number of confs: 697 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045876 none NC1=CN(CC(=O)NCCNC(=O)C2=CC(=O)[N-]O2)N=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'C.2', 'N.pl3', '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', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 8, 1, 6, 6, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 8, 33, 33, 33, 89, 131, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 1, 8, 8, 33, 89, 89, 131, 131, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 19, 20, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 774 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045876 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045876 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045876/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045876 Building REAL250005045877 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045877' /scratch/stefan/7916127/working/building/REAL250005045877 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045877 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045877/0 /scratch/stefan/7916127/working/building/REAL250005045877 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1033 `/scratch/stefan/7916127/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=NON=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045877.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045877 none NC1=NON=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 87, 87, 87, 43, 28, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 89, 89, 87, 43, 43, 28, 28, 9, 1] 89 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]) total number of confs: 304 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045877 none NC1=NON=C1C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.2', 'N.2', 'O.3', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 8, 12, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 6, 6, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 41, 83, 83, 83, 89, 89, 89, 89, 89, 1, 1, 5, 29, 29, 41, 41, 83, 89] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 20, 21] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045877 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045877 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045877/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045877 Building REAL250005045878 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045878' /scratch/stefan/7916127/working/building/REAL250005045878 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045878 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045878/0 /scratch/stefan/7916127/working/building/REAL250005045878 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1034 `/scratch/stefan/7916127/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(COC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045878.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045878 none O=C(COC(F)(F)F)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 12, 5, 15, 15, 15, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 3, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 167, 201, 201, 201, 201, 27, 16, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 167, 167, 73, 27, 27, 16, 16, 4, 1] 201 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]) total number of confs: 705 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045878 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045878 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045878/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045878 Building REAL250005045879 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045879' /scratch/stefan/7916127/working/building/REAL250005045879 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045879 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045879/0 /scratch/stefan/7916127/working/building/REAL250005045879 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1035 `/scratch/stefan/7916127/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)[C@@H]1CNC(=O)N1)C1=CC(=O)[N-]O1) `REAL250005045879.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045879 none O=C(NCCNC(=O)[C@@H]1CNC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 9, 9, 28, 39, 99, 99, 99, 153, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 9, 28, 28, 39, 39, 99, 153, 153, 153, 153, 1] 153 rigid atoms, others: [1, 15, 16, 17, 18, 19, 20, 31] 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]) total number of confs: 509 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: REAL250005045879 none O=C(NCCNC(=O)[C@@H]1CNC(=O)N1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 8, 1, 11, 5, 7, 5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [6, 7, 4, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 88, 64, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 144, 153, 153, 153, 153, 153, 144, 88, 88, 64, 64, 12, 1, 1, 1, 1, 153] 153 rigid atoms, others: [6, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31]) total number of confs: 559 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045879 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045879 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045879/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045879 Building REAL250005045880 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045880' /scratch/stefan/7916127/working/building/REAL250005045880 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045880 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045880/0 /scratch/stefan/7916127/working/building/REAL250005045880 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1036 `/scratch/stefan/7916127/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1) `REAL250005045880.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045880 none O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [7, 1, 7, 7, 22, 37, 75, 75, 75, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 7, 22, 22, 37, 37, 75, 107, 107, 1] 107 rigid atoms, others: [1, 13, 14, 15, 16, 17, 18, 27] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26]) 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: REAL250005045880 none O=C(NCCNC(=O)C1=CN=CS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 11, 1, 1, 8, 1, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [103, 103, 60, 43, 12, 12, 1, 12, 1, 1, 1, 1, 1, 103, 107, 107, 107, 107, 107, 103, 60, 60, 42, 42, 12, 1, 1, 107] 107 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26] set([0, 1, 2, 3, 4, 5, 7, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27]) total number of confs: 377 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045880 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045880 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045880/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045880 Building REAL250005045881 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045881' /scratch/stefan/7916127/working/building/REAL250005045881 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045881 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045881/0 /scratch/stefan/7916127/working/building/REAL250005045881 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1037 `/scratch/stefan/7916127/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC[NH+]1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045881.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045881 none O=C(CC[NH+]1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 1, 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, 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: [32, 32, 32, 39, 39, 48, 48, 48, 48, 48, 21, 21, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 48, 48, 48, 48, 48, 48, 48, 48, 32, 21, 21, 21, 21, 11, 1] 48 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: 190 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045881 none O=C(CC[NH+]1CCCC1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 8, 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, 6, 7] dock color type numbers: [6, 7, 7, 7, 1, 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, 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: [24, 7, 5, 1, 1, 1, 1, 1, 1, 1, 24, 24, 38, 39, 39, 39, 39, 48, 48, 48, 48, 48, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 24, 39, 39, 39, 39, 39, 48] 48 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045881 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045881 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045881/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045881 Building REAL250005045882 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045882' /scratch/stefan/7916127/working/building/REAL250005045882 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045882 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045882/0 /scratch/stefan/7916127/working/building/REAL250005045882 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1038 `/scratch/stefan/7916127/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N) `REAL250005045882.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045882 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 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, 170, 170, 170, 121, 121, 121, 54, 36, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 170, 170, 170, 170, 170, 170, 121, 54, 54, 36, 36, 11, 1, 170, 170] 170 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: 487 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045882 none CC1=NNC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1N NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 8, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 6, 6] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 59, 90, 161, 161, 161, 170, 170, 170, 170, 170, 1, 1, 2, 2, 2, 1, 12, 58, 58, 90, 90, 161, 170, 2, 2] 170 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 610 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045882 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045882 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045882/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045882 Building REAL250005045883 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045883' /scratch/stefan/7916127/working/building/REAL250005045883 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045883 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045883/0 /scratch/stefan/7916127/working/building/REAL250005045883 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1039 `/scratch/stefan/7916127/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: [N-]=[N+]=NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045883.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045883 none [N-]=[N+]=NCCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['N.1', 'N.1', 'N.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 8, 8, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 148, 132, 65, 65, 65, 33, 20, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 148, 148, 132, 132, 65, 33, 33, 20, 20, 4, 1] 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]) total number of confs: 700 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045883 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045883 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045883/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045883 Building REAL250005045884 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045884' /scratch/stefan/7916127/working/building/REAL250005045884 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045884 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045884/0 /scratch/stefan/7916127/working/building/REAL250005045884 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1040 `/scratch/stefan/7916127/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045884.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045884 none C#CCOCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 158, 115, 47, 47, 47, 19, 10, 1, 2, 1, 2, 1, 1, 1, 1, 1, 1, 201, 201, 201, 115, 115, 47, 19, 19, 10, 10, 2, 1] 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]) total number of confs: 806 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045884 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045884 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045884/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045884 Building REAL250005045885 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045885' /scratch/stefan/7916127/working/building/REAL250005045885 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045885 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045885/0 /scratch/stefan/7916127/working/building/REAL250005045885 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1041 `/scratch/stefan/7916127/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC1=NN=CO1)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045885.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045885 none O=C(CC1=NN=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 155, 201, 201, 201, 201, 23, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 155, 155, 201, 59, 23, 23, 14, 14, 4, 1] 201 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045885 none O=C(CC1=NN=CO1)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'O.3', 'N.am', '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'] dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 12, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 4, 1, 1, 1, 1, 1, 1, 32, 32, 119, 143, 201, 201, 201, 201, 201, 201, 201, 201, 4, 4, 1, 32, 119, 119, 143, 143, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 22] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 778 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045885 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045885 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045885/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045885 Building REAL250005045886 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045886' /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL250005045886 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045886/0 /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1042 `/scratch/stefan/7916127/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCO)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045886.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045886 none CN(CCO)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', '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', '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, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 6, 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 231 conformations in input total number of sets (complete confs): 231 using faster count positions algorithm for large data unique positions, atoms: [64, 55, 64, 65, 77, 32, 32, 32, 12, 9, 2, 3, 1, 3, 1, 1, 1, 1, 1, 1, 64, 64, 64, 65, 65, 77, 77, 231, 55, 55, 32, 12, 12, 9, 9, 3, 1] 231 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: 565 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `1' /scratch/stefan/7916127/working/building/REAL250005045886/1 /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 1 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1043 `/scratch/stefan/7916127/working/3D/1043' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@H+](CCO)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045886.mol2' -> `1.mol2' `temp.mol2' -> `REAL250005045886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.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: REAL250005045886 none C[N@H+](CCO)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 4, 7, 7, 6, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [28, 26, 28, 28, 28, 28, 21, 21, 21, 11, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 84, 26, 26, 21, 11, 11, 10, 10, 3, 1] 84 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: 192 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 mkdir: created directory `2' /scratch/stefan/7916127/working/building/REAL250005045886/2 /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 2 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1044 `/scratch/stefan/7916127/working/3D/1044' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@@H+](CCO)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045886.mol2' -> `2.mol2' `temp.mol2' -> `REAL250005045886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045886/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045886 none C[N@@H+](CCO)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'N.4', 'H', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 1, 7, 7, 7, 4, 7, 7, 6, 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 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [28, 26, 28, 28, 28, 28, 21, 21, 21, 11, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 84, 26, 26, 21, 11, 11, 10, 10, 3, 1] 84 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: 192 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045886 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045886 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 1: /scratch/stefan/7916127/working/building/REAL250005045886/1.* 0: /scratch/stefan/7916127/working/building/REAL250005045886/0.* 2: /scratch/stefan/7916127/working/building/REAL250005045886/2.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045886 Building REAL250005045887 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045887' /scratch/stefan/7916127/working/building/REAL250005045887 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045887 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045887/0 /scratch/stefan/7916127/working/building/REAL250005045887 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1045 `/scratch/stefan/7916127/working/3D/1045' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCNC(=O)C1CCCS1)C1=CC(=O)[N-]O1) `REAL250005045887.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045887 none O=C(NCCNC(=O)C1CCCS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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, 5, 8, 1, 11, 5, 5, 5, 5, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [9, 1, 9, 9, 28, 40, 95, 95, 95, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 9, 28, 28, 40, 40, 95, 144, 144, 144, 144, 144, 144, 144, 1] 144 rigid atoms, others: [32, 1, 13, 14, 15, 16, 17, 18] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 475 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: REAL250005045887 none O=C(NCCNC(=O)C1CCCS1)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'S.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, 5, 8, 1, 11, 5, 5, 5, 5, 14, 1, 1, 1, 11, 8, 12, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 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] 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: [139, 139, 89, 62, 12, 12, 1, 12, 1, 1, 1, 1, 1, 139, 144, 144, 144, 144, 144, 139, 89, 89, 62, 62, 12, 1, 1, 1, 1, 1, 1, 1, 144] 144 rigid atoms, others: [6, 8, 9, 10, 11, 12, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 7, 32, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 539 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045887 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045887 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045887/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045887 Building REAL250005045888 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045888' /scratch/stefan/7916127/working/building/REAL250005045888 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045888 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045888/0 /scratch/stefan/7916127/working/building/REAL250005045888 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1046 `/scratch/stefan/7916127/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)CC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045888.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045888 none COC(=O)CC(C)C(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 146, 201, 104, 47, 104, 47, 47, 20, 12, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 146, 146, 104, 104, 104, 104, 47, 20, 20, 12, 12, 4, 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: 831 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045888 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045888 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045888/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045888 Building REAL250005045889 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045889' /scratch/stefan/7916127/working/building/REAL250005045889 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045889 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045889/0 /scratch/stefan/7916127/working/building/REAL250005045889 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1047 `/scratch/stefan/7916127/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045889.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045889 none COC(C)(C)CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.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, 5, 5, 5, 1, 11, 8, 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, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 192, 112, 191, 191, 54, 54, 54, 24, 17, 3, 4, 1, 4, 1, 1, 1, 1, 1, 1, 201, 201, 201, 192, 192, 192, 192, 192, 192, 112, 112, 54, 24, 24, 17, 17, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045889 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045889 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045889/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045889 Building REAL250005045890 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045890' /scratch/stefan/7916127/working/building/REAL250005045890 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045890 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045890/0 /scratch/stefan/7916127/working/building/REAL250005045890 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1048) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1048 `/scratch/stefan/7916127/working/3D/1048' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045890.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045890 none CC(O)CCC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 6, 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 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [200, 148, 201, 142, 74, 74, 74, 35, 23, 6, 7, 1, 7, 1, 1, 1, 1, 1, 1, 201, 201, 200, 197, 603, 169, 169, 142, 142, 74, 35, 35, 23, 23, 7, 1] 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]) total number of confs: 1576 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045890 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045890 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045890/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045890 Building REAL250005045891 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045891' /scratch/stefan/7916127/working/building/REAL250005045891 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045891 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045891/0 /scratch/stefan/7916127/working/building/REAL250005045891 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1049) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1049 `/scratch/stefan/7916127/working/3D/1049' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCS(O)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1) `REAL250005045891.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 Warning: Using closest atom type 60 for atom 3 Warning: Using closest atom type 60 for atom 3 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045891 none CCS(O)=CC(=O)NCCNC(=O)C1=CC(=O)[N-]O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'O.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 12, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 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] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 168, 168, 168, 104, 104, 104, 37, 24, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 168, 168, 104, 37, 37, 24, 24, 8, 1] 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]) total number of confs: 727 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045891 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045891 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045891/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045891 Building REAL250005045892 mkdir: created directory `/scratch/stefan/7916127/working/building/REAL250005045892' /scratch/stefan/7916127/working/building/REAL250005045892 /scratch/stefan/7916127/working /scratch/stefan/7916127 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005045892 mkdir: created directory `0' /scratch/stefan/7916127/working/building/REAL250005045892/0 /scratch/stefan/7916127/working/building/REAL250005045892 /scratch/stefan/7916127/working /scratch/stefan/7916127 Protomer 0 (index: 1050) Found valid previously generated 3D confromation in /scratch/stefan/7916127/working/3D/1050 `/scratch/stefan/7916127/working/3D/1050' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1) `REAL250005045892.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005045892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7916127/working/building/REAL250005045892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045892 none NC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 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] 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, 123, 123, 123, 123, 69, 69, 69, 37, 26, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 69, 37, 37, 26, 26, 9, 1, 123] 123 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]) total number of confs: 342 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005045892 none NC1=CN=CC(C(=O)NCCNC(=O)C2=CC(=O)[N-]O2)=C1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 12, 1, 6, 6, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [4, 7, 7, 3, 7, 7, 7, 6, 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] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 33, 59, 117, 117, 117, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 5, 33, 33, 59, 59, 117, 123, 1] 123 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 20, 21, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7916127/working/building/REAL250005045892 /scratch/stefan/7916127/working /scratch/stefan/7916127 Finished preparing REAL250005045892 Recording results /scratch/stefan/7916127/working /scratch/stefan/7916127 Appending to /scratch/stefan/7916127/finished/xaaaaah.* 0: /scratch/stefan/7916127/working/building/REAL250005045892/0.* Removing working files in /scratch/stefan/7916127/working/building/REAL250005045892 /scratch/stefan/7916127 Compressing combined databse files /scratch/stefan/7916127/finished/xaaaaah.db2.gz /scratch/stefan/7916127/finished/xaaaaah.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7916127/finished) ======================================================= Finalizing... removed `/scratch/stefan/7916127/working/3D/1051' removed directory: `/scratch/stefan/7916127/working/3D' `/scratch/stefan/7916127/working/protonate' -> `/scratch/stefan/7916127/archive' `/scratch/stefan/7916127/working/input-smiles.ism' -> `/scratch/stefan/7916127/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7916127/working/building' rmdir: removing directory, `/scratch/stefan/7916127/working' ls: No match. ls: No match.